Tue May 14 10:11:32 UTC 2024 I: starting to build paleomix/trixie/arm64 on jenkins on '2024-05-14 10:11' Tue May 14 10:11:32 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_15/42602/console.log Tue May 14 10:11:32 UTC 2024 I: Downloading source for trixie/paleomix=1.3.8-1 --2024-05-14 10:11:32-- http://deb.debian.org/debian/pool/main/p/paleomix/paleomix_1.3.8-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2466 (2.4K) [text/prs.lines.tag] Saving to: ‘paleomix_1.3.8-1.dsc’ 0K .. 100% 351M=0s 2024-05-14 10:11:32 (351 MB/s) - ‘paleomix_1.3.8-1.dsc’ saved [2466/2466] Tue May 14 10:11:32 UTC 2024 I: paleomix_1.3.8-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: paleomix Binary: paleomix Architecture: any Version: 1.3.8-1 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: 9f201401a7f59b6e213ee8ff2bf264fd19177e37 1137201 paleomix_1.3.8.orig.tar.gz 5837230ee5ed9d68a491eb3ab743c7215dc6490b 10960 paleomix_1.3.8-1.debian.tar.xz Checksums-Sha256: 7bead15d96027aecea8462ea1a219f4a7c5356536679118140ad6390e01413ca 1137201 paleomix_1.3.8.orig.tar.gz ae3343fa66c4e838ea50b5f236dbd6b4313d860217497ca186b5f3cdd7983231 10960 paleomix_1.3.8-1.debian.tar.xz Files: 6e07794044685a77751e6552c52fa7dc 1137201 paleomix_1.3.8.orig.tar.gz 4a3053bb0892de279ffcbd0cd6548d39 10960 paleomix_1.3.8-1.debian.tar.xz Dgit: 6a230d34dae397a3f8909aa0df7d33a26da7efcf debian archive/debian/1.3.8-1 https://git.dgit.debian.org/paleomix -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmSGQdUUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqE8w//eoLD3s0By/yXXbRCvvDBsC7My4TG NoCdgQ4UZGQCM5FhjPcFFLuq93PtBM9gWWFb2fhSvLMxRpHPrh8RU9xCU7NXCj5e Y5PXHCuYoZuaKDIj+1BUOlEU3qk0zlmmBMxUtDOG6cfvhz7C2XPgAt6PDm5nu54z Sbc8xsQjYdBb713hrPFruw2WbUJefp47BTcGMG5HYxA8kLX7BXuooI+qEG8Re19b av9gkr6UiOgQKaYMqjPCBA9kG0tJugeW3rozj/1Lpk5L/czuoz8A5HJrESCs2XlW G2rwQyU+63tbn/+SYiQHNXxy+ISXwUfITL5FtfcgHAr4y6Cs52x9NaxmEdI1vM7T Q15NpD+pjTyqlRq4cIEn4OQoVQEFmogGR2O4MYrnjJs9GwDLhtxML6uNnjEIeIE/ cP/I7SlLoWee/Ay4Q3iQ+dd+pm3OOQJKl1MefmPGAaYk9O2HbM/3FbyicERU42WO 4958IiRjIxWUEcygPfnDlUI1pP5XCJhmwbvLtjz99YtIAjZavlzB1d1xCbpcOiGo KCx57gbfRj7Qg/dCdr2dKFOBz1e+gwLOutvwtWGAWWnbSZqkJvvhXhHnQLLl9YbG kpvHvEQ1XWa5q3SUYuZYVnu45fwKt/PGLq/U4VYZxM08hNhtVTvdq+7vh7Y0Vuub NyC4MRgY27cpxoc= =+PO5 -----END PGP SIGNATURE----- Tue May 14 10:11:32 UTC 2024 I: Checking whether the package is not for us Tue May 14 10:11:32 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Tue May 14 10:11:32 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Tue May 14 10:14:27 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 16 04:34:34 -12 2025 I: pbuilder-time-stamp: 1750091674 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [paleomix_1.3.8-1.dsc] I: copying [./paleomix_1.3.8.orig.tar.gz] I: copying [./paleomix_1.3.8-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jun 11 21:51:17 2023 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_1.3.8-1.dsc: no acceptable signature found dpkg-source: info: extracting paleomix in paleomix-1.3.8 dpkg-source: info: unpacking paleomix_1.3.8.orig.tar.gz dpkg-source: info: unpacking paleomix_1.3.8-1.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/2020893/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d24da7b5e7d04a64a13e931d65fecdf9' 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='2020893' 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.0Dhgvwoo/pbuilderrc_Y1CF --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0Dhgvwoo/b1 --logfile b1/build.log paleomix_1.3.8-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink01-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 13 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2020893/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 ... 19744 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} fonts-dejavu-mono{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} libamd-comgr2{a} libamdhip64-5{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2-data{a} libasound2t64{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbarclay-java{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0.10{a} libcom-err2{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} libcups2t64{a} libcurl3t64-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} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{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} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhts3t64{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm17t64{a} liblog4j2-java{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{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} libopenmpi3t64{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} libpmix2t64{a} libpng16-16t64{a} libpopt0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librdmacm1t64{a} libreadline8t64{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1t64{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libvulkan1{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} netbase{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-coloredlogs{a} python3-configargparse{a} python3-distutils{a} python3-humanfriendly{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{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} tzdata{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 krb5-locales 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 mesa-vulkan-drivers publicsuffix python3-pygments r-base-core wget xauth xdg-user-dirs 0 packages upgraded, 246 newly installed, 0 to remove and 0 not upgraded. Need to get 185 MB of archives. After unpacking 785 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpopt0 arm64 1.19+dfsg-1+b1 [42.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 rsync arm64 3.3.0-1 [401 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-1.1 [27.0 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.14.0-1+b2 [73.4 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.7p1-4 [902 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.80.2-1 [1393 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 shared-mime-info arm64 2.4-4 [755 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-3+b3 [130 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 gtk-update-icon-cache arm64 3.24.41-4 [46.2 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 at-spi2-common all 2.52.0-1 [166 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 bowtie2 arm64 2.5.3-1 [1339 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 71 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 java-common all 0.75 [6640 B] Get: 78 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.99-1 [1293 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.0.3-1 [50.3 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre-headless arm64 17.0.11+9-1 [42.8 MB] Get: 83 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.17-75 [3068 B] Get: 84 http://deb.debian.org/debian trixie/main arm64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libatk1.0-0t64 arm64 2.52.0-1 [49.2 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-13+b2 [112 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-13+b2 [42.4 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.14.10-4+b1 [195 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-13+b2 [45.7 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libcups2t64 arm64 2.4.7-1.2+b1 [230 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.52.2+ds-1 [206 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.52.2+ds-1 [45.5 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.52.2+ds-1 [33.0 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libxcomposite1 arm64 1:0.4.5-1+b1 [15.0 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2+b1 [20.5 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libxcursor1 arm64 1:1.2.1-1+b1 [35.8 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libxdamage1 arm64 1:1.1.6-1+b1 [15.6 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.1-1 [77.5 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libxinerama1 arm64 2:1.1.4-3+b1 [16.0 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libxrandr2 arm64 2:1.5.4-1 [35.7 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libgtk2.0-0t64 arm64 2.24.33-4 [1663 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1+b1 [41.7 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 128 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libglapi-mesa arm64 24.0.6-1+b1 [46.8 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.7-1+b1 [232 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3-1+b1 [9080 B] Get: 139 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.3.280.0-1 [119 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [18.7 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.120-2 [21.1 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-12 [21.3 MB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 24.0.6-1+b1 [7020 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 24.0.6-1+b1 [150 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1+b1 [31.0 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libgl1 arm64 1.7.0-1+b1 [90.9 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libasound2t64 arm64 1.2.11-1+b1 [334 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libgif7 arm64 5.2.2-1 [43.7 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libxtst6 arm64 2:1.2.3-1.1+b1 [25.9 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 openjdk-17-jre arm64 17.0.11+9-1 [174 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 default-jre arm64 2:1.17-75 [1056 B] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [125 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [54.3 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 50.0-2+b1 [58.2 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 50.0-2+b1 [315 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 50.0-2+b1 [66.6 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.10.0-1+b1 [18.0 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.2-3 [580 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b1 [12.1 MB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1 [21.4 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 5.7.0-1 [57.6 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 5.7.1-2 [276 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-3 [8698 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.16.0+ds-5 [938 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libopenmpi3t64 arm64 4.1.6-13.3 [2170 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 4.1.6-13.3 [225 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 examl arm64 3.0.22-5 [799 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 190 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 libcommons-lang3-java all 3.14.0-1 [621 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libfreemarker-java all 2.3.32-2 [1546 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libcommons-codec-java all 1.16.0-1 [297 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 libbarclay-java all 5.0.0+dfsg-1 [108 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 libcommons-compress-java all 1.25.0-1 [635 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 libcommons-io-java all 2.16.1-1 [480 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 208 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-5 [405 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 217 http://deb.debian.org/debian trixie/main arm64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto7t64 arm64 2.28.8-1 [269 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 libmbedx509-1t64 arm64 2.28.8-1 [131 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 libmbedtls14t64 arm64 2.28.8-1 [160 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2+b1 [985 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 libncbi-ngs3 arm64 3.0.3+dfsg-7 [141 kB] Get: 224 http://deb.debian.org/debian trixie/main arm64 libngs-jni arm64 3.0.3+dfsg-7 [23.6 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 libngs-java arm64 3.0.3+dfsg-7 [110 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 227 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.2.0-2 [28.3 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 libsnappy-jni arm64 1.1.10.5-2 [6440 B] Get: 229 http://deb.debian.org/debian trixie/main arm64 libsnappy-java all 1.1.10.5-2 [87.5 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 libhtsjdk-java all 4.1.0+dfsg-1 [1833 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 libgkl-java all 0.8.11+dfsg-2 [24.7 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 234 http://deb.debian.org/debian trixie/main arm64 libpicard-java all 3.1.1+dfsg-1 [1743 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 picard-tools all 3.1.1+dfsg-1 [311 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 python3-humanfriendly all 10.0-5 [85.4 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 python3-configargparse all 1.7-1 [31.3 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 240 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.0+ds-1+b2 [4209 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 7.4.4-3 [239 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 python3-ruamel.yaml.clib arm64 0.2.8+ds-1 [156 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 python3-ruamel.yaml all 0.18.6+ds-3 [145 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 python3-setproctitle arm64 1.3.3-1+b2 [19.5 kB] Fetched 185 MB in 2s (104 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 ... 19744 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20060 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21052 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpopt0:arm64. Preparing to unpack .../001-libpopt0_1.19+dfsg-1+b1_arm64.deb ... Unpacking libpopt0:arm64 (1.19+dfsg-1+b1) ... Selecting previously unselected package rsync. Preparing to unpack .../002-rsync_3.3.0-1_arm64.deb ... Unpacking rsync (3.3.0-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.2.1-3_arm64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. 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Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../042-adwaita-icon-theme_46.0-1_all.deb ... Unpacking adwaita-icon-theme (46.0-1) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../043-at-spi2-common_2.52.0-1_all.deb ... Unpacking at-spi2-common (2.52.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../044-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../045-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../046-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../047-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. 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Setting up libasound2-data (1.2.11-1) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1+b2) ... Setting up libglib2.0-0t64:arm64 (2.80.2-1) ... No schema files found: doing nothing. Setting up libasound2t64:arm64 (1.2.11-1+b1) ... Setting up libmunge2:arm64 (0.5.15-4) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:arm64 (2:4.35-1.1+b1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:arm64 (0.8-13+b2) ... Setting up libdbus-1-3:arm64 (1.14.10-4+b1) ... Setting up libfribidi0:arm64 (1.0.13-3+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up libhwloc15:arm64 (2.10.0-1+b1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:arm64 (2.0.3-1) ... 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Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libfido2-1:arm64 (1.14.0-1+b2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libsnappy-jni (1.1.10.5-2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libpopt0:arm64 (1.19+dfsg-1+b1) ... 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+b1) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up libatk1.0-0t64:arm64 (2.52.0-1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libedit2:arm64 (3.1-20230828-1+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-13+b2) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libnss3:arm64 (2:3.99-1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... 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 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libllvm17t64:arm64 (1:17.0.6-12) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up shared-mime-info (2.4-4) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:arm64 (2.4.120-2) ... Setting up libmbedtls14t64:arm64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-3+b3) ... Setting up libsnappy-java (1.1.10.5-2) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.16.0-1) ... Setting up libxcomposite1:arm64 (1:0.4.5-1+b1) ... Setting up libavahi-client3:arm64 (0.8-13+b2) ... Setting up rsync (3.3.0-1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdrm-amdgpu1:arm64 (2.4.120-2) ... Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:arm64 (2:1.8.7-1+b1) ... Setting up libibverbs1:arm64 (50.0-2+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:arm64 (2.4.120-2) ... Setting up libxdamage1:arm64 (1:1.1.6-1+b1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libcommons-compress-java (1.25.0-1) ... Setting up ibverbs-providers:arm64 (50.0-2+b1) ... Setting up libcommons-io-java (2.16.1-1) ... Setting up libdrm-radeon1:arm64 (2.4.120-2) ... Setting up openssh-client (1:9.7p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libpango-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libgl1-mesa-dri:arm64 (24.0.6-1+b1) ... Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-5) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-3+b1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:arm64 (535.171.04-1) ... Setting up adwaita-icon-theme (46.0-1) ... 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+b1) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b1) ... Setting up libxrandr2:arm64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:arm64 (17.0.11+9-1) ... 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 libhttpclient-java (4.5.14-1) ... Setting up libhts3t64:arm64 (1.19+ds-1.1+b1) ... Setting up librdmacm1t64:arm64 (50.0-2+b1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libpangoft2-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libcups2t64:arm64 (2.4.7-1.2+b1) ... Setting up libhsakmt1:arm64 (5.7.0-1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-7) ... Setting up libfabric1:arm64 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libngs-jni:arm64 (3.0.3+dfsg-7) ... Setting up libglx-mesa0:arm64 (24.0.6-1+b1) ... Setting up libxi6:arm64 (2:1.8.1-1) ... Setting up libglx0:arm64 (1.7.0-1+b1) ... Setting up libxtst6:arm64 (2:1.2.3-1.1+b1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libxcursor1:arm64 (1:1.2.1-1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libhwloc-plugins:arm64 (2.10.0-1+b1) ... Setting up bowtie2 (2.5.3-1) ... Setting up python3-packaging (24.0-1) ... Setting up libgl1:arm64 (1.7.0-1+b1) ... Setting up python3-humanfriendly (10.0-5) ... Setting up python3-setproctitle:arm64 (1.3.3-1+b2) ... Setting up libgtk2.0-0t64:arm64 (2.24.33-4) ... Setting up libpmix2t64:arm64 (5.0.2-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libngs-java:arm64 (3.0.3+dfsg-7) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up libhtsjdk-java (4.1.0+dfsg-1) ... Setting up libbarclay-java (5.0.0+dfsg-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-configargparse (1.7-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libgkl-java (0.8.11+dfsg-2) ... Setting up python3-pytest (7.4.4-3) ... Setting up python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... Setting up libpicard-java (3.1.1+dfsg-1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-ruamel.yaml (0.18.6+ds-3) ... Setting up dh-python (6.20240422) ... Setting up libucx0:arm64 (1.16.0+ds-5) ... Setting up libopenmpi3t64:arm64 (4.1.6-13.3) ... Setting up openmpi-bin (4.1.6-13.3) ... 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 (3.0.22-5) ... Processing triggers for libc-bin (2.38-10) ... Processing triggers for ca-certificates-java (20240118) ... 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:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.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:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.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: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_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:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.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:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.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 default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:arm64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up picard-tools (3.1.1+dfsg-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/paleomix-1.3.8/ && 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_1.3.8-1_source.changes dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.3.8-1 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:311: python3.11 setup.py clean running clean removing '/build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-aarch64' 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:311: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix copying paleomix/yaml.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix copying paleomix/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix copying paleomix/nodegraph.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix copying paleomix/node.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix copying paleomix/main.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix copying paleomix/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/vcf_to_fasta.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/vcf_filter.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/validate_fastq.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/rmdup_collapsed.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/gtf_to_bed.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/factory.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/dupcheck.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/depths.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/coverage.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/cleanup.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources copying paleomix/resources/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines copying paleomix/pipelines/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/validation.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/sequences.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/samtools.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/raxml.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/picard.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/phylip.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/newick.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/mapdamage.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/mafft.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/formats.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/examl.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/commands.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bwa.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bowtie2.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bedtools.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/adapterremoval.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/versions.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/vcfwrap.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/vcffilter.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/utilities.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/timer.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/text.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/testing.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/system.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/sequences.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/sampling.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/rtools.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/procs.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/makefile.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/logging.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/fileutils.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/bedtools.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/bamfiles.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/argparse.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/sets.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/pprint.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/command.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/builder.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/coverage.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/common.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/database.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/config.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/common.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_tped.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_mito.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_db.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/mkfile.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/makefile.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/example.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/config.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/trim_pipeline.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/paths.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/nodes.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/mkfile.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/makefile.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/config.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/summary.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/report.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/nuclear.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/common.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/admixture.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/phylo.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/msa.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/genotype.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/target.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/summary.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/statistics.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/sample.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/reads.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/prefix.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/library.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/lane.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/phylip.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/newick.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/msa.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/fastq.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/fasta.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/_graph.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/_common.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/__init__.py -> /build/reproducible-path/paleomix-1.3.8/.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:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline.data' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline.prefixes' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.prefixes' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline.prefixes' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline.prefixes' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline.prefixes' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.alignment' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.alignment' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.alignment' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.phylogeny' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.phylogeny' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.phylogeny' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.reports.zonkey' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.reports.zonkey' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.reports.zonkey' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.reports.zonkey' to be distributed and are already explicitly excluding 'paleomix.resources.reports.zonkey' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.rscripts.common' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.common' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.rscripts.common' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.rscripts.common' to be distributed and are already explicitly excluding 'paleomix.resources.rscripts.common' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.rscripts.zonkey' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.zonkey' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.rscripts.zonkey' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.rscripts.zonkey' to be distributed and are already explicitly excluding 'paleomix.resources.rscripts.zonkey' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline copying paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline creating /build/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data creating /build/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes copying paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny copying paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.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/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/reports creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey copying paleomix/resources/reports/zonkey/report.css -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common copying paleomix/resources/rscripts/common/requires.r -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common creating /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/admixture.r -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/coverage.r -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/pca.r -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/tinytree.r -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/treemix.r -> /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/paleomix-1.3.8' PATH=/build/reproducible-path/paleomix-1.3.8/bin/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild pybuild:308: cp -a README.rst /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build; I: pybuild base:311: cd /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/paleomix-1.3.8 configfile: setup.cfg collected 1492 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%] ........................................................................ [ 19%] ................ [ 20%] tests/atomiccmd_test/pprint_test.py .................................... [ 23%] .. [ 23%] tests/atomiccmd_test/sets_test.py ...................................... [ 26%] ............ [ 26%] tests/common_tests/bedtools_test.py ............................... [ 28%] tests/common_tests/fileutils_test.py ................................... [ 31%] ...................................................................... [ 35%] 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/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py:24: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 import pipes -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 1440 passed, 1 xfailed, 51 xpassed, 1 warning in 22.34s ============ make[1]: Leaving directory '/build/reproducible-path/paleomix-1.3.8' 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:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/paleomix-1.3.8/debian/paleomix running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing 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:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline.data' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.bam_pipeline.prefixes' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.prefixes' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.bam_pipeline.prefixes' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.bam_pipeline.prefixes' to be distributed and are already explicitly excluding 'paleomix.resources.examples.bam_pipeline.prefixes' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.alignment' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.alignment' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.alignment' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.phylogeny' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.phylogeny' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.phylogeny' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' to be distributed and are already explicitly excluding 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.reports.zonkey' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.reports.zonkey' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.reports.zonkey' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.reports.zonkey' to be distributed and are already explicitly excluding 'paleomix.resources.reports.zonkey' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.rscripts.common' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.common' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.rscripts.common' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.rscripts.common' to be distributed and are already explicitly excluding 'paleomix.resources.rscripts.common' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'paleomix.resources.rscripts.zonkey' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.zonkey' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'paleomix.resources.rscripts.zonkey' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'paleomix.resources.rscripts.zonkey' to be distributed and are already explicitly excluding 'paleomix.resources.rscripts.zonkey' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running install_lib creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11 creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/README.rst -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__pycache__/pipeline.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__pycache__/main.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__pycache__/yaml.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__pycache__/nodegraph.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__pycache__/node.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/sets.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/builder.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/pprint.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/command.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/builder.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/command.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/sets.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/vcfwrap.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/vcffilter.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/timer.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/bamfiles.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/argparse.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/rtools.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/logging.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/system.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/text.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/sequences.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/sampling.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/makefile.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/testing.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/bedtools.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/versions.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/procs.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/utilities.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/fileutils.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/phylip.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/_graph.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/newick.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/msa.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/fastq.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/fasta.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/_common.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/_common.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/_graph.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/fasta.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/fastq.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/msa.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/newick.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/formats/phylip.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/argparse.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/bamfiles.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/bedtools.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/fileutils.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/logging.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/makefile.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/procs.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/rtools.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/sampling.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/sequences.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/system.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/testing.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/text.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/timer.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/utilities.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/vcffilter.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/vcfwrap.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/common/versions.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/newick.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/examl.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/phylip.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/raxml.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/formats.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/mafft.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/sequences.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bedtools.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/commands.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/mapdamage.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/picard.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/adapterremoval.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/validation.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bowtie2.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bwa.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/samtools.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/adapterremoval.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/bedtools.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/bowtie2.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/bwa.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/commands.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/examl.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/formats.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/mafft.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/mapdamage.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/newick.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/phylip.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/picard.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/raxml.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/samtools.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/sequences.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodes/validation.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/trim_pipeline.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/mkfile.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/config.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/nodes.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/makefile.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/pipeline.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/paths.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/summary.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/statistics.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/target.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/prefix.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/sample.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/library.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/lane.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/reads.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/lane.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/library.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/prefix.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/reads.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/sample.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/statistics.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/summary.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/target.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/config.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/makefile.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/mkfile.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/nodes.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/paths.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/trim_pipeline.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/makefile.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/config.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/mkfile.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/example.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/pipeline.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/phylo.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/msa.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/genotype.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/genotype.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/msa.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/phylo.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/config.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/example.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/makefile.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/mkfile.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_tped.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_mito.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_db.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/common.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/database.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/config.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/pipeline.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/summary.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/admixture.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/report.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/nuclear.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/mitochondria.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/common.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/admixture.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/common.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/nuclear.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/report.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/summary.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_db.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_mito.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_tped.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/common.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/config.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/database.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipelines/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/treemix.r -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/tinytree.r -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/pca.r -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/coverage.r -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/admixture.r -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/common copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common/requires.r -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/common creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports/zonkey copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey/report.css -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports/zonkey creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/resources/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/validate_fastq.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/vcf_to_fasta.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/vcf_filter.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/rmdup_collapsed.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/depths.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/coverage.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/cleanup.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/factory.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats creating /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/common.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/coverage.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/__init__.cpython-311.pyc -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/common.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/coverage.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/cleanup.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/coverage.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/depths.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/dupcheck.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/factory.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/gtf_to_bed.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/rmdup_collapsed.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/validate_fastq.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/vcf_filter.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/tools/vcf_to_fasta.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/__init__.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/main.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/node.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/nodegraph.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/pipeline.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/reproducible-path/paleomix-1.3.8/.pybuild/cpython3_3.11/build/paleomix/yaml.py -> /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/builder.py to builder.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/command.py to command.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/pprint.py to pprint.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/sets.py to sets.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/_common.py to _common.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/_graph.py to _graph.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/fasta.py to fasta.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/fastq.py to fastq.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/msa.py to msa.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/newick.py to newick.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/phylip.py to phylip.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/argparse.py to argparse.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/bamfiles.py to bamfiles.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/bedtools.py to bedtools.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/fileutils.py to fileutils.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/logging.py to logging.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/makefile.py to makefile.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/procs.py to procs.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/rtools.py to rtools.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/sampling.py to sampling.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/sequences.py to sequences.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/system.py to system.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/testing.py to testing.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/text.py to text.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/timer.py to timer.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/utilities.py to utilities.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/vcffilter.py to vcffilter.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/vcfwrap.py to vcfwrap.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/versions.py to versions.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/adapterremoval.py to adapterremoval.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bedtools.py to bedtools.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bowtie2.py to bowtie2.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bwa.py to bwa.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/commands.py to commands.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/examl.py to examl.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/formats.py to formats.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/mafft.py to mafft.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/mapdamage.py to mapdamage.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/newick.py to newick.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/phylip.py to phylip.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/picard.py to picard.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/raxml.py to raxml.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/samtools.py to samtools.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/sequences.py to sequences.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/validation.py to validation.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/lane.py to lane.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/library.py to library.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/prefix.py to prefix.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/reads.py to reads.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/sample.py to sample.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/statistics.py to statistics.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/summary.py to summary.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/target.py to target.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/config.py to config.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/makefile.py to makefile.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/mkfile.py to mkfile.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/nodes.py to nodes.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/paths.py to paths.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/trim_pipeline.py to trim_pipeline.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/genotype.py to genotype.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/msa.py to msa.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/phylo.py to phylo.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/config.py to config.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/example.py to example.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/makefile.py to makefile.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/mkfile.py to mkfile.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/admixture.py to admixture.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/common.py to common.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/mitochondria.py to mitochondria.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/nuclear.py to nuclear.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/report.py to report.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/summary.py to summary.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_db.py to build_db.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_mito.py to build_mito.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_tped.py to build_tped.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/common.py to common.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/config.py to config.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/database.py to database.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/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/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/common.py to common.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/coverage.py to coverage.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/cleanup.py to cleanup.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/coverage.py to coverage.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/depths.py to depths.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/dupcheck.py to dupcheck.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/factory.py to factory.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/gtf_to_bed.py to gtf_to_bed.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/rmdup_collapsed.py to rmdup_collapsed.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/validate_fastq.py to validate_fastq.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/vcf_filter.py to vcf_filter.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/vcf_to_fasta.py to vcf_to_fasta.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/main.py to main.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/node.py to node.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodegraph.py to nodegraph.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/reproducible-path/paleomix-1.3.8/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/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix-1.3.8.egg-info Skipping SOURCES.txt running install_scripts Installing paleomix script to /build/reproducible-path/paleomix-1.3.8/debian/paleomix/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/paleomix-1.3.8' dh_install find debian -name LICENSE -delete find debian -name README.rst -delete make[1]: Leaving directory '/build/reproducible-path/paleomix-1.3.8' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/paleomix-1.3.8' 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 334,827 speedup is 326.34 # 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/reproducible-path/paleomix-1.3.8' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/paleomix-1.3.8' dh_python3 --verbose --shebang=/usr/bin/python3 D: dh_python3 dh_python3:179: version: 6.20240422 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: 3.11,3.12 (default=3.11) D: dh_python3 debhelper:174: source=paleomix, binary packages=['paleomix'] D: dh_python3 dh_python3:204: processing package paleomix... D: dh_python3 fs:50: moving files from debian/paleomix/usr/lib/python3.11/dist-packages to debian/paleomix/usr/lib/python3/dist-packages/ I: dh_python3 tools:113: replacing shebang in debian/paleomix/usr/bin/paleomix D: dh_python3 fs:335: package paleomix details = {'requires.txt': {'debian/paleomix/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/requires.txt'}, 'egg-info': {'debian/paleomix/usr/lib/python3/dist-packages/paleomix-1.3.8.egg-info/PKG-INFO'}, '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:103: 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:253: D={'python3:any', 'python3-configargparse', 'python3-pysam', 'python3-ruamel.yaml', 'python3-setproctitle', 'python3-coloredlogs'}; R=[]; S=[]; E=[], B=[]; RT=[] make[1]: Leaving directory '/build/reproducible-path/paleomix-1.3.8' 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/reproducible-path/paleomix-1.3.8' 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/reproducible-path/paleomix-1.3.8' 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_1.3.8-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../paleomix_1.3.8-1_arm64.buildinfo dpkg-genchanges --build=binary -O../paleomix_1.3.8-1_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: including full 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/2020893 and its subdirectories I: Current time: Mon Jun 16 04:37:25 -12 2025 I: pbuilder-time-stamp: 1750091845 Tue May 14 10:14:28 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Tue May 14 10:14:28 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Tue May 14 10:16:05 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Tue May 14 10:16:06 UTC 2024 I: paleomix_1.3.8-1_arm64.changes: Format: 1.8 Date: Sun, 11 Jun 2023 23:37:02 +0200 Source: paleomix Binary: paleomix Architecture: arm64 Version: 1.3.8-1 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 Changes: paleomix (1.3.8-1) unstable; urgency=medium . * New upstream version Checksums-Sha1: b2313d4f8d9f6ccccf02734949c92f2fa9e99348 11944 paleomix_1.3.8-1_arm64.buildinfo d2b34a4bb16eecdde5afdd2f721aeee59acfa02f 983864 paleomix_1.3.8-1_arm64.deb Checksums-Sha256: 9754ec165ae81c2f678840d17adb3096c5002f7640b301ef9407e1ccf45ac5f6 11944 paleomix_1.3.8-1_arm64.buildinfo 88b413d492605eb27eeecbf328959ce156a0e85d50a0b3dfe8b82a60dfec7efc 983864 paleomix_1.3.8-1_arm64.deb Files: 9a82128a6a1841766be59248e91e5200 11944 science optional paleomix_1.3.8-1_arm64.buildinfo 9094ba1464116213f5ee45eb922bba8b 983864 science optional paleomix_1.3.8-1_arm64.deb Tue May 14 10:16:07 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_15-42602.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0Dhgvwoo/paleomix_1.3.8-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0Dhgvwoo/paleomix_1.3.8-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0Dhgvwoo/paleomix_1.3.8-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0Dhgvwoo/b1/paleomix_1.3.8-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.0Dhgvwoo/b2/paleomix_1.3.8-1_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: 0.423s) 0.423s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 777ms CPU time consumed: 773ms Tue May 14 10:16:08 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Tue May 14 10:16:08 UTC 2024 I: paleomix from trixie built successfully and reproducibly on arm64. Tue May 14 10:16:11 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 14 10:16:11 UTC 2024 I: Submitting 16K b1/paleomix_1.3.8-1_arm64.buildinfo.asc Tue May 14 10:16:14 UTC 2024 I: Submitting 16K b2/paleomix_1.3.8-1_arm64.buildinfo.asc Tue May 14 10:16:16 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 14 10:16:16 UTC 2024 I: Done submitting .buildinfo files. Tue May 14 10:16:16 UTC 2024 I: Removing signed paleomix_1.3.8-1_arm64.buildinfo.asc files: removed './b1/paleomix_1.3.8-1_arm64.buildinfo.asc' removed './b2/paleomix_1.3.8-1_arm64.buildinfo.asc'