I: pbuilder: network access will be disabled during build I: Current time: Thu May 4 17:29:54 -12 2023 I: pbuilder-time-stamp: 1683264594 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [paleomix_1.3.7-3.dsc] I: copying [./paleomix_1.3.7.orig.tar.gz] I: copying [./paleomix_1.3.7-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 14 07:06:42 2023 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./paleomix_1.3.7-3.dsc: no acceptable signature found dpkg-source: info: extracting paleomix in paleomix-1.3.7 dpkg-source: info: unpacking paleomix_1.3.7.orig.tar.gz dpkg-source: info: unpacking paleomix_1.3.7-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying xfail_command_tests.patch dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3775129/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='69c63d1524aa43e1adbc75f934b3e868' 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='3775129' 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.emgkI0zE/pbuilderrc_NrGw --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.emgkI0zE/b1 --logfile b1/build.log paleomix_1.3.7-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3775129/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: amd64 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 ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-coloredlogs; however: Package python3-coloredlogs is not installed. pbuilder-satisfydepends-dummy depends on python3-configargparse; however: Package python3-configargparse is not installed. pbuilder-satisfydepends-dummy depends on python3-ruamel.yaml; however: Package python3-ruamel.yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-setproctitle; however: Package python3-setproctitle is not installed. pbuilder-satisfydepends-dummy depends on default-jre-headless; however: Package default-jre-headless is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync is not installed. pbuilder-satisfydepends-dummy depends on examl; however: Package examl is not installed. pbuilder-satisfydepends-dummy depends on picard-tools; however: Package picard-tools is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie2{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} examl{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} ibverbs-providers{a} intltool-debian{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbarclay-java{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0.8{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcups2{a} libcurl3-gnutls{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libjbig0{a} libjoptsimple-java{a} libjpeg62-turbo{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm15{a} liblog4j2-java{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmongodb-java{a} libmunge2{a} libncbi-ngs3{a} libncbi-vdb3{a} libnghttp2-14{a} libngs-java{a} libngs-jni{a} libnl-3-200{a} libnl-route-3-200{a} libnspr4{a} libnss3{a} libnuma1{a} libopenmpi3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{a} libpcsclite1{a} libpicard-java{a} libpipeline1{a} libpixman-1-0{a} libpmix2{a} libpng16-16{a} libpopt0{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librdmacm1{a} libreadline8{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libwebp7{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml2{a} libxnvctrl0{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} ncbi-vdb-data{a} ocl-icd-libopencl1{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} picard-tools{a} po-debconf{a} python3{a} python3-attr{a} python3-coloredlogs{a} python3-configargparse{a} python3-distutils{a} python3-humanfriendly{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pysam{a} python3-pytest{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-setproctitle{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} rsync{a} sensible-utils{a} shared-mime-info{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus fonts-dejavu-extra libarchive-cpio-perl libatk-wrapper-java-jni libgail-common libgdk-pixbuf2.0-bin libgkl-jni libglib2.0-data libgtk2.0-bin libldap-common libltdl-dev libmail-sendmail-perl librsvg2-common libsasl2-modules lynx publicsuffix python3-pygments r-base-core wget xauth xdg-user-dirs 0 packages upgraded, 237 newly installed, 0 to remove and 0 not upgraded. Need to get 170 MB of archives. After unpacking 644 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpopt0 amd64 1.19+dfsg-1 [43.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 rsync amd64 3.2.7-1 [417 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.5.0-3+b2 [1409 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 75 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.6+10-1 [168 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 150 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 examl amd64 3.0.22-3+b2 [951 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libfreemarker-java all 2.3.31-2 [1528 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libbarclay-java all 4.1.0+dfsg-1 [103 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-5 [153 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-5 [23.4 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-5 [110 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libgkl-java all 0.8.10+dfsg-3 [25.0 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libpicard-java all 2.27.5+dfsg-2 [1725 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 picard-tools all 2.27.5+dfsg-2 [311 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 python3-humanfriendly all 10.0-3 [85.2 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 python3-configargparse all 1.5.3-1 [26.1 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 227 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 python3-py all 1.11.0-1 [89.2 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 python3-pytest all 7.2.1-2 [236 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml.clib amd64 0.2.7-1+b2 [113 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 python3-ruamel.yaml all 0.17.21-1 [103 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 python3-setproctitle amd64 1.3.1-1+b2 [17.9 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 170 MB in 9s (18.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libpopt0:amd64 (1.19+dfsg-1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up rsync (3.2.7-1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-5) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-5) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:amd64 (525.85.05-1) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-5) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up python3-humanfriendly (10.0-3) ... Setting up python3-setproctitle:amd64 (1.3.1-1+b2) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up libbarclay-java (4.1.0+dfsg-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-configargparse (1.5.3-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libgkl-java (0.8.10+dfsg-3) ... Setting up python3-pytest (7.2.1-2) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up python3-ruamel.yaml.clib:amd64 (0.2.7-1+b2) ... Setting up libpicard-java (2.27.5+dfsg-2) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up examl (3.0.22-3+b2) ... Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jre:amd64 (17.0.6+10-1) ... Setting up default-jre (2:1.17-74) ... Setting up picard-tools (2.27.5+dfsg-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/paleomix-1.3.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../paleomix_1.3.7-3_source.changes dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.3.7-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/paleomix-1.3.7/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/yaml.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/nodegraph.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/node.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/main.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/vcf_filter.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/validate_fastq.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/factory.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/dupcheck.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/depths.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/coverage.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/cleanup.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources copying paleomix/resources/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines copying paleomix/pipelines/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/validation.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/sequences.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/samtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/raxml.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/picard.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/phylip.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/newick.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/mapdamage.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/mafft.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/formats.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/examl.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/commands.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bwa.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bowtie2.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bedtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/adapterremoval.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/versions.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/vcfwrap.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/vcffilter.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/utilities.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/timer.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/text.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/testing.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/system.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/sequences.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/sampling.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/rtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/procs.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/makefile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/logging.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/fileutils.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/bedtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/bamfiles.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/argparse.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/sets.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/pprint.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/command.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/builder.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/database.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/config.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_tped.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_mito.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_db.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/mkfile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/makefile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/example.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/config.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/trim_pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/paths.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/nodes.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/mkfile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/makefile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/config.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/summary.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/report.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/nuclear.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/admixture.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/phylo.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/msa.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/genotype.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/target.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/summary.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/statistics.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/sample.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/reads.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/prefix.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/library.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/lane.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/phylip.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/newick.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/msa.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/fastq.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/fasta.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/_graph.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/_common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats running egg_info creating paleomix.egg-info writing paleomix.egg-info/PKG-INFO writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing requirements to paleomix.egg-info/requires.txt writing top-level names to paleomix.egg-info/top_level.txt writing manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'paleomix/yaml/CHANGES' warning: no files found matching 'paleomix/yaml/LICENSE' warning: no files found matching 'paleomix/yaml/PKG-INFO' warning: no files found matching 'paleomix/yaml/README' warning: no files found matching 'pylint.conf' adding license file 'LICENSE' writing manifest file 'paleomix.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.reports.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.reports.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.reports.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.reports.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.common' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.common' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.common' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.common' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline copying paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes copying paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny copying paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey copying paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common copying paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey debian/rules override_dh_auto_test make[1]: Entering directory '/build/paleomix-1.3.7' PATH=/build/paleomix-1.3.7/bin/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild pybuild:307: cp -a README.rst /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build; I: pybuild base:240: cd /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/paleomix-1.3.7, configfile: setup.cfg collected 1494 items tests/node_test.py ..................................................... [ 3%] ......................................... [ 6%] tests/nodegraph_test.py ......... [ 6%] tests/atomiccmd_test/builder_test.py ................................... [ 9%] ...................................................... [ 12%] tests/atomiccmd_test/command_test.py ................................... [ 15%] ........................................................................ [ 20%] ................ [ 21%] tests/atomiccmd_test/pprint_test.py .................................... [ 23%] .. [ 23%] tests/atomiccmd_test/sets_test.py ...................................... [ 26%] ............ [ 26%] tests/common_tests/bedtools_test.py ............................... [ 29%] tests/common_tests/fileutils_test.py ................................... [ 31%] ...................................................................... [ 36%] tests/common_tests/makefile_test.py .................................... [ 38%] ........................................................................ [ 43%] ........................................................................ [ 48%] ........................................................................ [ 52%] ........................................................................ [ 57%] ............................... [ 59%] tests/common_tests/sampling_test.py ........................ [ 61%] tests/common_tests/sequences_test.py ................................... [ 63%] ............... [ 64%] tests/common_tests/text_test.py ....................................... [ 67%] tests/common_tests/utilities_test.py ................................... [ 69%] ........................................................................ [ 74%] .. [ 74%] tests/common_tests/versions_test.py .................................... [ 77%] ............................................................ [ 81%] tests/common_tests/formats_tests/fasta_test.py ......................... [ 82%] ............. [ 83%] tests/common_tests/formats_tests/fastq_test.py ......................... [ 85%] ........... [ 86%] tests/common_tests/formats_tests/msa_test.py ........................... [ 87%] ................... [ 89%] tests/common_tests/formats_tests/newick_test.py ........................ [ 90%] ........................................................................ [ 95%] ...... [ 95%] tests/common_tests/formats_tests/phylip_test.py ........ [ 96%] tests/tools_test/factory_test.py xXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [ 99%] XXXXXXXXXXXXX [100%] =============================== warnings summary =============================== paleomix/atomiccmd/pprint.py:24 /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py:24: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 import pipes .pybuild/cpython3_3.11/build/tests/node_test.py::test_dir /usr/lib/python3/dist-packages/_pytest/python.py:199: PytestReturnNotNoneWarning: Expected None, but .pybuild/cpython3_3.11/build/tests/node_test.py::test_dir returned '/build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/tests', which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? warnings.warn( .pybuild/cpython3_3.11/build/tests/node_test.py::test_file /usr/lib/python3/dist-packages/_pytest/python.py:199: PytestReturnNotNoneWarning: Expected None, but .pybuild/cpython3_3.11/build/tests/node_test.py::test_file returned '/build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/tests/data', which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 1442 passed, 1 xfailed, 51 xpassed, 3 warnings in 27.30s =========== make[1]: Leaving directory '/build/paleomix-1.3.7' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/paleomix/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/paleomix-1.3.7/debian/paleomix running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing paleomix.egg-info/PKG-INFO writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing requirements to paleomix.egg-info/requires.txt writing top-level names to paleomix.egg-info/top_level.txt reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'paleomix/yaml/CHANGES' warning: no files found matching 'paleomix/yaml/LICENSE' warning: no files found matching 'paleomix/yaml/PKG-INFO' warning: no files found matching 'paleomix/yaml/README' warning: no files found matching 'pylint.conf' adding license file 'LICENSE' writing manifest file 'paleomix.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.reports.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.reports.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.reports.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.reports.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.common' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.common' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.common' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.common' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running install_lib creating /build/paleomix-1.3.7/debian/paleomix/usr creating /build/paleomix-1.3.7/debian/paleomix/usr/lib creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11 creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/README.rst -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/main.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/yaml.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/nodegraph.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/node.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/sets.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/builder.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/pprint.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/command.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/builder.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/command.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/sets.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/vcfwrap.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/vcffilter.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/timer.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/bamfiles.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/argparse.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/rtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/logging.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/system.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/text.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/sequences.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/sampling.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/makefile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/testing.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/bedtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/versions.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/procs.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/utilities.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/fileutils.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/phylip.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/_graph.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/newick.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/msa.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/fastq.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/fasta.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/_common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/_common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/_graph.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/fasta.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/fastq.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/msa.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/newick.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/phylip.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/argparse.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/bamfiles.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/bedtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/fileutils.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/logging.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/makefile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/procs.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/rtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/sampling.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/sequences.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/system.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/testing.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/text.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/timer.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/utilities.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/vcffilter.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/vcfwrap.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/versions.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/newick.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/examl.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/phylip.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/raxml.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/formats.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/mafft.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/sequences.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bedtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/commands.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/mapdamage.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/picard.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/adapterremoval.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/validation.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bowtie2.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bwa.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/samtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/adapterremoval.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/bedtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/bowtie2.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/bwa.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/commands.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/examl.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/formats.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/mafft.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/mapdamage.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/newick.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/phylip.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/picard.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/raxml.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/samtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/sequences.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/validation.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/trim_pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/mkfile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/config.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/nodes.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/makefile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/paths.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/summary.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/statistics.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/target.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/prefix.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/sample.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/library.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/lane.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/reads.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/lane.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/library.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/prefix.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/reads.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/sample.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/statistics.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/summary.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/target.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/config.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/makefile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/mkfile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/nodes.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/paths.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/trim_pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/makefile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/config.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/mkfile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/example.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/phylo.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/msa.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/genotype.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/genotype.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/msa.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/phylo.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/config.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/example.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/makefile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/mkfile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_tped.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_mito.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_db.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/database.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/config.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/summary.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/admixture.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/report.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/nuclear.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/mitochondria.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/admixture.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/nuclear.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/report.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/summary.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_db.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_mito.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_tped.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/config.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/database.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/common creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports/zonkey creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/validate_fastq.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/vcf_to_fasta.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/vcf_filter.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/rmdup_collapsed.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/depths.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/coverage.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/cleanup.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/factory.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/coverage.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/cleanup.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/coverage.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/depths.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/dupcheck.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/factory.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/validate_fastq.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/vcf_filter.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/main.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/node.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodegraph.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/yaml.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/builder.py to builder.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/command.py to command.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/pprint.py to pprint.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/sets.py to sets.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/_common.py to _common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/_graph.py to _graph.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/fasta.py to fasta.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/fastq.py to fastq.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/msa.py to msa.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/newick.py to newick.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/phylip.py to phylip.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/argparse.py to argparse.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/bamfiles.py to bamfiles.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/bedtools.py to bedtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/fileutils.py to fileutils.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/logging.py to logging.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/makefile.py to makefile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/procs.py to procs.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/rtools.py to rtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/sampling.py to sampling.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/sequences.py to sequences.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/system.py to system.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/testing.py to testing.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/text.py to text.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/timer.py to timer.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/utilities.py to utilities.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/vcffilter.py to vcffilter.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/vcfwrap.py to vcfwrap.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/versions.py to versions.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/adapterremoval.py to adapterremoval.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bedtools.py to bedtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bowtie2.py to bowtie2.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bwa.py to bwa.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/commands.py to commands.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/examl.py to examl.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/formats.py to formats.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/mafft.py to mafft.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/mapdamage.py to mapdamage.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/newick.py to newick.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/phylip.py to phylip.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/picard.py to picard.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/raxml.py to raxml.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/samtools.py to samtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/sequences.py to sequences.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/validation.py to validation.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/lane.py to lane.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/library.py to library.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/prefix.py to prefix.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/reads.py to reads.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/sample.py to sample.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/statistics.py to statistics.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/summary.py to summary.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/target.py to target.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/config.py to config.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/makefile.py to makefile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/mkfile.py to mkfile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/nodes.py to nodes.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/paths.py to paths.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/trim_pipeline.py to trim_pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/genotype.py to genotype.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/msa.py to msa.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/phylo.py to phylo.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/config.py to config.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/example.py to example.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/makefile.py to makefile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/mkfile.py to mkfile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/admixture.py to admixture.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/common.py to common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/mitochondria.py to mitochondria.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/nuclear.py to nuclear.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/report.py to report.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/summary.py to summary.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_db.py to build_db.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_mito.py to build_mito.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_tped.py to build_tped.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/common.py to common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/config.py to config.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/database.py to database.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py to synthesize_reads.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/common.py to common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/coverage.py to coverage.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/cleanup.py to cleanup.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/coverage.py to coverage.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/depths.py to depths.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/dupcheck.py to dupcheck.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/factory.py to factory.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/gtf_to_bed.py to gtf_to_bed.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/rmdup_collapsed.py to rmdup_collapsed.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/validate_fastq.py to validate_fastq.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/vcf_filter.py to vcf_filter.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/vcf_to_fasta.py to vcf_to_fasta.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/main.py to main.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/node.py to node.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodegraph.py to nodegraph.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/yaml.py to yaml.cpython-311.pyc running install_egg_info Copying paleomix.egg-info to /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix-1.3.7.egg-info Skipping SOURCES.txt running install_scripts Installing paleomix script to /build/paleomix-1.3.7/debian/paleomix/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/paleomix-1.3.7' dh_install find debian -name LICENSE -delete find debian -name README.rst -delete make[1]: Leaving directory '/build/paleomix-1.3.7' debian/rules override_dh_installdocs make[1]: Entering directory '/build/paleomix-1.3.7' dh_installdocs # since tests dir contains empty files which are used afterwards for # testing and dh_installdocs is ignoring empty files we need to make # sure all files are really copied rsync -a -v tests debian/paleomix/usr/share/doc/paleomix sending incremental file list tests/atomiccmd_test/ tests/common_tests/ tests/common_tests/formats_tests/ tests/data/ tests/data/empty_file_1 tests/data/empty_file_2 sent 950 bytes received 76 bytes 2,052.00 bytes/sec total size is 334,745 speedup is 326.26 # test runner is seeking for paleomix modules in source - we use inside the installed package ### sed -i 's:(find paleomix -mindepth 1:(find /usr/lib/python*/dist-packages/paleomix -mindepth 1:' debian/*/usr/share/doc/*/tests/run #echo "====== Also empty files belong to the docs ======" #find debian -name "empty_file*" #find debian -name "timestamp_*" #echo "====== Hope something was printed between these lines ====" # # This test tries to execute setup.sh which does not work outside source directory find debian/paleomix/usr/share/doc/ -name fileutils_test.py -delete find debian/paleomix/usr/share/doc/ -name setup.h -delete make[1]: Leaving directory '/build/paleomix-1.3.7' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/paleomix-1.3.7' dh_python3 --verbose --shebang=/usr/bin/python3 D: dh_python3 dh_python3:179: version: 5.20230130 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '--verbose', '--shebang=/usr/bin/python3'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang='/usr/bin/python3', ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=None) D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11) D: dh_python3 debhelper:183: source=paleomix, binary packages=['paleomix'] D: dh_python3 dh_python3:204: processing package paleomix... D: dh_python3 fs:52: moving files from debian/paleomix/usr/lib/python3.11/dist-packages to debian/paleomix/usr/lib/python3/dist-packages/ I: dh_python3 tools:114: replacing shebang in debian/paleomix/usr/bin/paleomix D: dh_python3 fs:400: package paleomix details = {'requires.txt': {'debian/paleomix/usr/lib/python3/dist-packages/paleomix-1.3.7.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package paleomix D: dh_python3 pydist:173: trying to find dependency for coloredlogs>=10.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for configargparse>=0.13.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for pysam>=0.10.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for ruamel.yaml>=0.16.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for setproctitle>=1.1.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 depends:281: D={'python3-pysam', 'python3-configargparse', 'python3-coloredlogs', 'python3-ruamel.yaml', 'python3:any', 'python3-setproctitle'}; R=[]; S=[]; E=[], B=[]; RT=[] make[1]: Leaving directory '/build/paleomix-1.3.7' dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/paleomix-1.3.7' dh_fixperms for rs in `find debian -iname "*.r"` ; do \ if head -n 1 $rs | grep -q '^#!/usr/bin/.*Rscript' ; then \ chmod +x $rs ; \ else \ chmod -x $rs ; \ fi ; \ done make[1]: Leaving directory '/build/paleomix-1.3.7' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'paleomix' in '../paleomix_1.3.7-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../paleomix_1.3.7-3_amd64.buildinfo dpkg-genchanges --build=binary -O../paleomix_1.3.7-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3775129 and its subdirectories I: Current time: Thu May 4 17:32:52 -12 2023 I: pbuilder-time-stamp: 1683264772