https://launchpad.net/ubuntu/+source/atropos/1.1.31+dfsg-3/+build/23749370 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-066 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_212~550~ubuntu20.04.1 python3-lpbuildd_212~550~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 15 May 20:28:42 ntpdate[1455793]: adjust time server 10.211.37.1 offset -0.001515 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 --image-type chroot /home/buildd/filecache-default/6534a4ff757521d8f8bbfb46d24688ecd71c00f8 Creating target for build PACKAGEBUILD-23749370 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 Starting target for build PACKAGEBUILD-23749370 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 'deb http://ftpmaster.internal/ubuntu kinetic main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-security main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-updates main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23749370 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 Updating target for build PACKAGEBUILD-23749370 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main riscv64 Packages [1291 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 Packages [13.0 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5698 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 Packages [118 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [57.9 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 Packages [616 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [263 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted riscv64 Packages [720 B] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted Translation-en [6720 B] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse riscv64 Packages [3168 B] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse Translation-en [6248 B] Fetched 22.2 MB in 32s (694 kB/s) Reading package lists... W: Target Packages (main/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: util-linux-extra The following packages will be upgraded: binutils binutils-common binutils-riscv64-linux-gnu bsdutils cpp-11 dash debianutils dpkg dpkg-dev g++-11 gcc-11 gcc-11-base gcc-12-base libasan6 libassuan0 libatomic1 libbinutils libblkid1 libcc1-0 libctf-nobfd0 libctf0 libdpkg-perl libgcc-11-dev libgcc-s1 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libjson-c5 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libreadline8 libseccomp2 libsmartcols1 libsqlite3-0 libssl3 libstdc++-11-dev libstdc++6 libtinfo6 libuuid1 libzstd1 linux-libc-dev lto-disabled-list mount ncurses-base ncurses-bin openssl pinentry-curses readline-common util-linux 59 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 57.5 MB of archives. After this operation, 984 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 bsdutils riscv64 1:2.38-4ubuntu1 [91.0 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main riscv64 debianutils riscv64 5.7-0.2 [102 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libzstd1 riscv64 1.5.2+dfsg-1 [318 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 dpkg riscv64 1.21.7ubuntu3 [1300 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 dash riscv64 0.5.11+git20210903+057cd650a4ed-8 [83.8 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 ncurses-bin riscv64 6.3+20220423-2 [176 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libblkid1 riscv64 2.38-4ubuntu1 [149 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libmount1 riscv64 2.38-4ubuntu1 [157 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libsmartcols1 riscv64 2.38-4ubuntu1 [102 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 util-linux-extra riscv64 2.38-4ubuntu1 [103 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 util-linux riscv64 2.38-4ubuntu1 [1142 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpam0g riscv64 1.4.0-13ubuntu1 [55.6 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpam-modules-bin riscv64 1.4.0-13ubuntu1 [36.9 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpam-modules riscv64 1.4.0-13ubuntu1 [263 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 mount riscv64 2.38-4ubuntu1 [130 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libatomic1 riscv64 12.1.0-2ubuntu1 [7846 B] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 gcc-12-base riscv64 12.1.0-2ubuntu1 [18.8 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libstdc++6 riscv64 12.1.0-2ubuntu1 [674 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgomp1 riscv64 12.1.0-2ubuntu1 [110 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libcc1-0 riscv64 12.1.0-2ubuntu1 [42.8 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgcc-s1 riscv64 12.1.0-2ubuntu1 [44.0 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgpg-error0 riscv64 1.45-2 [62.7 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpam-runtime all 1.4.0-13ubuntu1 [40.2 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpcre2-8-0 riscv64 10.40-1 [141 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpcre3 riscv64 2:8.39-14 [171 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libncursesw6 riscv64 6.3+20220423-2 [127 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libncurses6 riscv64 6.3+20220423-2 [92.7 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libtinfo6 riscv64 6.3+20220423-2 [89.8 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libuuid1 riscv64 2.38-4ubuntu1 [26.2 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libp11-kit0 riscv64 0.24.1-1 [205 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgnutls30 riscv64 3.7.4-2ubuntu1 [875 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libip4tc2 riscv64 1.8.7-1ubuntu6 [18.0 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libjson-c5 riscv64 0.16-1 [29.3 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 readline-common all 8.1.2-1.2 [53.6 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libreadline8 riscv64 8.1.2-1.2 [130 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libseccomp2 riscv64 2.5.4-1ubuntu1 [44.0 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libsqlite3-0 riscv64 3.38.5-1 [572 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libssl3 riscv64 3.0.3-0ubuntu1 [1437 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 openssl riscv64 3.0.3-0ubuntu1 [1135 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpng16-16 riscv64 1.6.37-5 [174 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libctf-nobfd0 riscv64 2.38-4ubuntu1 [98.9 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libctf0 riscv64 2.38-4ubuntu1 [96.8 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 binutils-riscv64-linux-gnu riscv64 2.38-4ubuntu1 [911 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libbinutils riscv64 2.38-4ubuntu1 [485 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 binutils riscv64 2.38-4ubuntu1 [3090 B] Get:47 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 binutils-common riscv64 2.38-4ubuntu1 [214 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libasan6 riscv64 11.3.0-1ubuntu1 [2107 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main riscv64 g++-11 riscv64 11.3.0-1ubuntu1 [9302 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-11 riscv64 11.3.0-1ubuntu1 [15.9 MB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libstdc++-11-dev riscv64 11.3.0-1ubuntu1 [4775 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgcc-11-dev riscv64 11.3.0-1ubuntu1 [2396 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main riscv64 cpp-11 riscv64 11.3.0-1ubuntu1 [7990 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-11-base riscv64 11.3.0-1ubuntu1 [21.1 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 dpkg-dev all 1.21.7ubuntu3 [1070 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libdpkg-perl all 1.21.7ubuntu3 [236 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main riscv64 lto-disabled-list all 25 [12.6 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libassuan0 riscv64 2.5.5-3 [31.9 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 linux-libc-dev riscv64 5.15.0-28.29 [1302 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 pinentry-curses riscv64 1.2.0-1 [37.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.5 MB in 8s (6857 kB/s) (Reading database ... 13361 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.38-4ubuntu1_riscv64.deb ... Unpacking bsdutils (1:2.38-4ubuntu1) over (1:2.37.2-4ubuntu3) ... Setting up bsdutils (1:2.38-4ubuntu1) ... (Reading database ... 13361 files and directories currently installed.) Preparing to unpack .../debianutils_5.7-0.2_riscv64.deb ... Unpacking debianutils (5.7-0.2) over (5.5-1ubuntu2) ... Setting up debianutils (5.7-0.2) ... (Reading database ... 13360 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.2+dfsg-1_riscv64.deb ... Unpacking libzstd1:riscv64 (1.5.2+dfsg-1) over (1.4.8+dfsg-3build1) ... Setting up libzstd1:riscv64 (1.5.2+dfsg-1) ... (Reading database ... 13360 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.7ubuntu3_riscv64.deb ... Unpacking dpkg (1.21.7ubuntu3) over (1.21.1ubuntu2) ... Setting up dpkg (1.21.7ubuntu3) ... dpkg: warning: This system uses merged-usr-via-aliased-dirs, going behind dpkg's dpkg: warning: back, breaking its core assumptions. This can cause silent file dpkg: warning: overwrites and disappearances, and its general tools misbehavior. dpkg: warning: See . (Reading database ... 13364 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-8_riscv64.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-8) over (0.5.11+git20210903+057cd650a4ed-3build1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-8) ... (Reading database ... 13365 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.3+20220423-2_riscv64.deb ... Unpacking ncurses-bin (6.3+20220423-2) over (6.3-2) ... Setting up ncurses-bin (6.3+20220423-2) ... (Reading database ... 13365 files and directories currently installed.) Preparing to unpack .../libblkid1_2.38-4ubuntu1_riscv64.deb ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23749370 riscv64 kinetic-proposed -c chroot:build-PACKAGEBUILD-23749370 --arch=riscv64 --dist=kinetic-proposed --nolog atropos_1.1.31+dfsg-3.dsc Initiating build PACKAGEBUILD-23749370 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-066.buildd +==============================================================================+ | atropos 1.1.31+dfsg-3 (riscv64) Sun, 15 May 2022 20:34:27 +0000 | +==============================================================================+ Package: atropos Version: 1.1.31+dfsg-3 Source Version: 1.1.31+dfsg-3 Distribution: kinetic-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23749370/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/atropos-9Mu9vo/resolver-bDV387' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- atropos_1.1.31+dfsg-3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/atropos-9Mu9vo/atropos-1.1.31+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/atropos-9Mu9vo' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, cython3, python3-all-dev, python3-setuptools, python3-setuptools-scm, python3-wheel, python3-loguru, python3-xphyle, python3-pytest, python3-jinja2, python3-pysam, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, cython3, python3-all-dev, python3-setuptools, python3-setuptools-scm, python3-wheel, python3-loguru, python3-xphyle, python3-pytest, python3-jinja2, python3-pysam, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [448 B] Get:5 copy:/<>/apt_archive ./ Packages [522 B] Fetched 1927 B in 1s (3350 B/s) Reading package lists... Reading package lists... W: Target Packages (main/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore libldap-2.5-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python-babel-localedata python3 python3-all python3-all-dev python3-attr python3-babel python3-colorama python3-dev python3-distutils python3-iniconfig python3-jinja2 python3-lib2to3 python3-loguru python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-pokrok python3-py python3-pyparsing python3-pysam python3-pytest python3-setuptools python3-setuptools-scm python3-toml python3-tomli python3-tz python3-wheel python3-xphyle python3.10 python3.10-dev python3.10-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cython-doc dh-make flit python3-build python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc python-jinja2-doc subversion python-pyparsing-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu71 libjs-jquery libjs-sphinxdoc libjs-underscore libldap-2.5-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python-babel-localedata python3 python3-all python3-all-dev python3-attr python3-babel python3-colorama python3-dev python3-distutils python3-iniconfig python3-jinja2 python3-lib2to3 python3-loguru python3-markupsafe python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-pokrok python3-py python3-pyparsing python3-pysam python3-pytest python3-setuptools python3-setuptools-scm python3-toml python3-tomli python3-tz python3-wheel python3-xphyle python3.10 python3.10-dev python3.10-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 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21.3-1 [30.7 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 python3-pluggy all 1.0.0-1 [15.1 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-pokrok all 0.2.0-2 [10.8 kB] Get:88 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-py all 1.10.0-1 [71.9 kB] Get:89 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-pysam riscv64 0.17.0+ds-2build1 [1649 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-toml all 0.10.2-1 [16.5 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 python3-pytest all 6.2.5-2ubuntu1 [214 kB] Get:92 http://ftpmaster.internal/ubuntu kinetic/main riscv64 python3-setuptools all 59.6.0-1.2 [339 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-tomli all 1.2.2-2 [12.9 kB] Get:94 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-setuptools-scm all 6.4.2-1 [31.7 kB] Get:95 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-wheel all 0.37.1-2 [31.9 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 python3-xphyle all 4.4.1-3 [48.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.3 MB in 10s (4856 kB/s) Selecting previously unselected package libpython3.10-minimal:riscv64. 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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:riscv64 (1.2.1-1) ... Setting up media-types (8.0.0) ... Setting up libpipeline1:riscv64 (1.5.6-1) ... Setting up libicu71:riscv64 (71.1-3) ... Setting up libpsl5:riscv64 (0.21.0-1.2build2) ... Setting up bsdextrautils (2.38-4ubuntu1) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.7.1ubuntu1) ... Setting up libbrotli1:riscv64 (1.0.9-2build6) ... Setting up libnghttp2-14:riscv64 (1.47.0-1) ... Setting up libmagic1:riscv64 (1:5.41-4) ... Setting up libdeflate0:riscv64 (1.10-2) ... Setting up gettext-base (0.21-4ubuntu4) ... Setting up file (1:5.41-4) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:riscv64 (2.4.8-1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libsigsegv2:riscv64 (2.13-1ubuntu3) ... Setting up autopoint (0.21-4ubuntu4) ... Setting up libsasl2-2:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Setting up libssh-4:riscv64 (0.9.6-2build1) ... Setting up zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up libmpdec3:riscv64 (2.5.1-2build2) ... Setting up libsub-override-perl (0.09-2) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up libelf1:riscv64 (0.187-1) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1) ... Setting up libjs-underscore (1.13.3~dfsg+~1.11.4-1) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:riscv64 (0.187-1) ... Setting up gettext (0.21-4ubuntu4) ... Setting up libtool (2.4.7-4) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libldap-2.5-0:riscv64 (2.5.11+dfsg-1~exp1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.10-stdlib:riscv64 (3.10.4-4) ... Setting up libjs-sphinxdoc (4.5.0-3) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libpython3-stdlib:riscv64 (3.10.4-0ubuntu2) ... 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 libpython3.10:riscv64 (3.10.4-4) ... Setting up python3.10 (3.10.4-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:riscv64 (7.83.1-1) ... Setting up python3 (3.10.4-0ubuntu2) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.0.1-2build1) ... Setting up python3-tz (2022.1-1) ... Setting up dh-autoreconf (20) ... Setting up python3-pyparsing (3.0.7-2) ... Setting up cython3 (0.29.28-1ubuntu3) ... Setting up libpython3.10-dev:riscv64 (3.10.4-4) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-pluggy (1.0.0-1) ... Setting up python3.10-dev (3.10.4-4) ... Setting up python3-lib2to3 (3.10.4-0ubuntu1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-distutils (3.10.4-0ubuntu1) ... Setting up dh-python (5.20220403) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (21.2.0-1) ... Setting up python3-pokrok (0.2.0-2) ... Setting up libhts3:riscv64 (1.13+ds-2build2) ... Setting up python3-pysam (0.17.0+ds-2build1) ... Setting up libpython3-dev:riscv64 (3.10.4-0ubuntu2) ... Setting up python3-setuptools (59.6.0-1.2) ... Setting up python3-tomli (1.2.2-2) ... Setting up python3-py (1.10.0-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.4-1) ... Setting up python3-loguru (0.6.0-1) ... Setting up python3-all (3.10.4-0ubuntu2) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up python3-wheel (0.37.1-2) ... Setting up python3-jinja2 (3.0.3-1) ... Setting up python3-packaging (21.3-1) ... Setting up libpython3-all-dev:riscv64 (3.10.4-0ubuntu2) ... Setting up python3-dev (3.10.4-0ubuntu2) ... Setting up python3-xphyle (4.4.1-3) ... Setting up python3-all-dev (3.10.4-0ubuntu2) ... Setting up python3-pytest (6.2.5-2ubuntu1) ... Setting up python3-setuptools-scm (6.4.2-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.38-4ubuntu1 dpkg-dev_1.21.7ubuntu3 g++-11_11.3.0-1ubuntu1 gcc-11_11.3.0-1ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-1ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-28.29 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu2 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-4ubuntu4 autotools-dev_20220109.1 base-files_12ubuntu5 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Hash: SHA512 Format: 3.0 (quilt) Source: atropos Binary: atropos Architecture: any Version: 1.1.31+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/jdidion/atropos Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/atropos Vcs-Git: https://salsa.debian.org/med-team/atropos.git Testsuite: autopkgtest Testsuite-Triggers: python3-all, python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, cython3, python3-all-dev, python3-setuptools, python3-setuptools-scm, python3-wheel, python3-loguru, python3-xphyle, python3-pytest , python3-jinja2 , python3-pysam Package-List: atropos deb science optional arch=any Checksums-Sha1: 63d72403dc96e61ff368e989a3dd21f31b884846 3115688 atropos_1.1.31+dfsg.orig.tar.xz bde59085620b333502167548ec58704cd33f4cfc 6380 atropos_1.1.31+dfsg-3.debian.tar.xz Checksums-Sha256: d59fb286c59461cb87ca9c86aed09f3a108f92ba800a6de424a3dd65f88f704b 3115688 atropos_1.1.31+dfsg.orig.tar.xz a91895654074cb38388ab67ab1ea273fa8be72ec44567d96937e0a5aae2961c8 6380 atropos_1.1.31+dfsg-3.debian.tar.xz Files: a6e70957ca15bb86d62819e8d9926846 3115688 atropos_1.1.31+dfsg.orig.tar.xz 025a3cdf44ecf9d93a65b198b9bbef17 6380 atropos_1.1.31+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmJLLJwSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nx+G4QAKeCs58iKOKU4X4Hlv0BpfQ4hO52yqwd 7h4DQwosPsRQCXukPQESgooedv7doqvEWvDolJvyCgAeeiU3BSM0WQFMe+ErR1Ya Z1Zp4sHSRkJxNwtKWuW7uyEFYbQxZqyW7bu99W68xk6t50E7AzdfhshPOlUxIMXo xh3JoEgFGN3PDbibNxT/X/K/SZSlcCgzKeg0X+WjQLOdw+XhCIFmlUFHiuieSD+Z ve1nyCsxAnuFfEB6tJjDu7g11jFlzmXVpOVoFR3Pjgmvkq8m0l91e1HRtTqMcrPn 9j2TqzCUVe53ZeSogF/RzgOVYGvU7kWix3Wh2g+13x6Aq6Yuq3ZOkBQPvvfBuyCk LOIHAO+ybjI+mDL/yiq7MDjfoHUSM6cJC1Rd/b53FbFl0SuQY3HClSHdJ2sN1Klk tsDU0mzomQR7KumchN52mAMBknIy3xArlfnwhcJCa/rpqPJ2kclQ7WfXZm7CYhlv IiWLUzg+RdAd+PCDXsZadm7A75bHMtXm2e6EuE+PRT3ci0Q1PsfSPzjPIsrPzmTt 0uzLQj3igATIptBpm4S3Rtt7Nz3JNr0WbO9qQo88VtPz4Vy2eGTNQ6R8lZHEH+k3 oP3irrrgj++8ZIg89S32uuTDn1ZZtCkcSvlNSfpgtgHnGN7ZE31HKyCbl/1+Ltxj 0v5XFGx9AB4V =X2rL -----END PGP SIGNATURE----- gpgv: Signature made Mon Apr 4 17:36:28 2022 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./atropos_1.1.31+dfsg-3.dsc dpkg-source: info: extracting atropos in /<> dpkg-source: info: unpacking atropos_1.1.31+dfsg.orig.tar.xz dpkg-source: info: unpacking atropos_1.1.31+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3.10.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23749370 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23749370 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23749370 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package atropos dpkg-buildpackage: info: source version 1.1.31+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base:239: python3.10 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running clean removing '/<>/.pybuild/cpython3_3.10/build' (and everything under it) 'build/bdist.linux-riscv64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it rm -rf .pytest_cache rm -rf atropos.egg-info rm -f atropos/align/_align.c atropos/commands/trim/_qualtrim.c atropos/io/_seqio.c make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:239: python3.10 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:239: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running build running build_py creating /<>/.pybuild/cpython3_3.10/build/tests copying tests/__init__.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_commands.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_seqio.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_qualtrim.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_filters.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_trim.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_modifiers.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/utils.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_multicore.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_paired.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_colorspace.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_xopen.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_align.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_adapters.py -> /<>/.pybuild/cpython3_3.10/build/tests copying tests/test_atropos.py -> /<>/.pybuild/cpython3_3.10/build/tests creating /<>/.pybuild/cpython3_3.10/build/atropos copying atropos/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos copying atropos/_version.py -> /<>/.pybuild/cpython3_3.10/build/atropos creating /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/stats.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/cli.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/multicore.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/base.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/reports.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands copying atropos/commands/legacy_report.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands creating /<>/.pybuild/cpython3_3.10/build/atropos/align copying atropos/align/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/align creating /<>/.pybuild/cpython3_3.10/build/atropos/io copying atropos/io/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/io copying atropos/io/seqio.py -> /<>/.pybuild/cpython3_3.10/build/atropos/io copying atropos/io/progress.py -> /<>/.pybuild/cpython3_3.10/build/atropos/io copying atropos/io/compression.py -> /<>/.pybuild/cpython3_3.10/build/atropos/io creating /<>/.pybuild/cpython3_3.10/build/atropos/adapters copying atropos/adapters/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/adapters creating /<>/.pybuild/cpython3_3.10/build/atropos/util copying atropos/util/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/util copying atropos/util/colorspace.py -> /<>/.pybuild/cpython3_3.10/build/atropos/util creating /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/filters.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/cli.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/writers.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/multicore.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/qualtrim.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/modifiers.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim copying atropos/commands/trim/reports.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim creating /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc copying atropos/commands/qc/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc copying atropos/commands/qc/cli.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc copying atropos/commands/qc/reports.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc creating /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect copying atropos/commands/detect/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect copying atropos/commands/detect/cli.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect copying atropos/commands/detect/reports.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect creating /<>/.pybuild/cpython3_3.10/build/atropos/commands/error copying atropos/commands/error/__init__.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/error copying atropos/commands/error/cli.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/error copying atropos/commands/error/reports.py -> /<>/.pybuild/cpython3_3.10/build/atropos/commands/error copying atropos/adapters/sequencing_adapters.fa -> /<>/.pybuild/cpython3_3.10/build/atropos/adapters UPDATING /<>/.pybuild/cpython3_3.10/build/atropos/_version.py set /<>/.pybuild/cpython3_3.10/build/atropos/_version.py to '1.1.31' running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/atropos/align/_align.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/atropos/commands/trim/_qualtrim.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/atropos/io/_seqio.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling atropos/align/_align.pyx because it changed. Compiling atropos/commands/trim/_qualtrim.pyx because it changed. Compiling atropos/io/_seqio.pyx because it changed. [1/3] Cythonizing atropos/align/_align.pyx [2/3] Cythonizing atropos/commands/trim/_qualtrim.pyx [3/3] Cythonizing atropos/io/_seqio.pyx building 'atropos.align._align' extension creating build creating build/temp.linux-riscv64-3.10 creating build/temp.linux-riscv64-3.10/atropos creating build/temp.linux-riscv64-3.10/atropos/align riscv64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c atropos/align/_align.c -o build/temp.linux-riscv64-3.10/atropos/align/_align.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.10/atropos/align/_align.o -o /<>/.pybuild/cpython3_3.10/build/atropos/align/_align.cpython-310-riscv64-linux-gnu.so building 'atropos.commands.trim._qualtrim' extension creating build/temp.linux-riscv64-3.10/atropos/commands creating build/temp.linux-riscv64-3.10/atropos/commands/trim riscv64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c atropos/commands/trim/_qualtrim.c -o build/temp.linux-riscv64-3.10/atropos/commands/trim/_qualtrim.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.10/atropos/commands/trim/_qualtrim.o -o /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/_qualtrim.cpython-310-riscv64-linux-gnu.so building 'atropos.io._seqio' extension creating build/temp.linux-riscv64-3.10/atropos/io riscv64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c atropos/io/_seqio.c -o build/temp.linux-riscv64-3.10/atropos/io/_seqio.o riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.10/atropos/io/_seqio.o -o /<>/.pybuild/cpython3_3.10/build/atropos/io/_seqio.cpython-310-riscv64-linux-gnu.so running build_scripts creating build/scripts-3.10 copying and adjusting bin/atropos -> build/scripts-3.10 changing mode of build/scripts-3.10/atropos from 644 to 755 create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install --destdir=debian/atropos/ -a -O--buildsystem=pybuild I: pybuild base:239: /usr/bin/python3 setup.py install --root /<>/debian/atropos /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( 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 UPDATING /<>/.pybuild/cpython3_3.10/build/atropos/_version.py set /<>/.pybuild/cpython3_3.10/build/atropos/_version.py to '1.1.31' running build_ext running build_scripts running install_lib creating /<>/debian/atropos/usr creating /<>/debian/atropos/usr/lib creating /<>/debian/atropos/usr/lib/python3.10 creating /<>/debian/atropos/usr/lib/python3.10/dist-packages creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_commands.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_seqio.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_qualtrim.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_filters.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_trim.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_modifiers.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/utils.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_multicore.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_paired.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_colorspace.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_xopen.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_align.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_adapters.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests copying /<>/.pybuild/cpython3_3.10/build/tests/test_atropos.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos copying /<>/.pybuild/cpython3_3.10/build/atropos/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/filters.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/_qualtrim.cpython-310-riscv64-linux-gnu.so -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/cli.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/writers.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/multicore.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/qualtrim.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/modifiers.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/trim/reports.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc/cli.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/qc/reports.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/stats.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/cli.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect/cli.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/detect/reports.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/multicore.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/error/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/error/cli.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/error/reports.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/base.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/reports.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands copying /<>/.pybuild/cpython3_3.10/build/atropos/commands/legacy_report.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands copying /<>/.pybuild/cpython3_3.10/build/atropos/_version.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/align copying /<>/.pybuild/cpython3_3.10/build/atropos/align/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/align copying /<>/.pybuild/cpython3_3.10/build/atropos/align/_align.cpython-310-riscv64-linux-gnu.so -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/align creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io copying /<>/.pybuild/cpython3_3.10/build/atropos/io/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io copying /<>/.pybuild/cpython3_3.10/build/atropos/io/seqio.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io copying /<>/.pybuild/cpython3_3.10/build/atropos/io/progress.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io copying /<>/.pybuild/cpython3_3.10/build/atropos/io/compression.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io copying /<>/.pybuild/cpython3_3.10/build/atropos/io/_seqio.cpython-310-riscv64-linux-gnu.so -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/adapters copying /<>/.pybuild/cpython3_3.10/build/atropos/adapters/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/adapters copying /<>/.pybuild/cpython3_3.10/build/atropos/adapters/sequencing_adapters.fa -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/adapters creating /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/util copying /<>/.pybuild/cpython3_3.10/build/atropos/util/__init__.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/util copying /<>/.pybuild/cpython3_3.10/build/atropos/util/colorspace.py -> /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/util byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_commands.py to test_commands.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_seqio.py to test_seqio.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_qualtrim.py to test_qualtrim.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_filters.py to test_filters.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_trim.py to test_trim.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_modifiers.py to test_modifiers.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/utils.py to utils.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_multicore.py to test_multicore.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_paired.py to test_paired.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_colorspace.py to test_colorspace.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_xopen.py to test_xopen.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_align.py to test_align.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_adapters.py to test_adapters.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/tests/test_atropos.py to test_atropos.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/filters.py to filters.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/cli.py to cli.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/writers.py to writers.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/multicore.py to multicore.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/qualtrim.py to qualtrim.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/modifiers.py to modifiers.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/trim/reports.py to reports.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc/cli.py to cli.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/qc/reports.py to reports.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/stats.py to stats.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/cli.py to cli.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect/cli.py to cli.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/detect/reports.py to reports.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/multicore.py to multicore.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error/cli.py to cli.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/error/reports.py to reports.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/base.py to base.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/reports.py to reports.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/commands/legacy_report.py to legacy_report.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/_version.py to _version.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/align/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io/seqio.py to seqio.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io/progress.py to progress.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/io/compression.py to compression.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/adapters/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/util/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos/util/colorspace.py to colorspace.cpython-310.pyc running install_egg_info running egg_info creating atropos.egg-info writing atropos.egg-info/PKG-INFO writing dependency_links to atropos.egg-info/dependency_links.txt writing requirements to atropos.egg-info/requires.txt writing top-level names to atropos.egg-info/top_level.txt writing manifest file 'atropos.egg-info/SOURCES.txt' reading manifest file 'atropos.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'README.rst' warning: no files found matching 'LICENSE.txt' warning: no files found matching 'atropos/report/templates/*' adding license file 'LICENSE' writing manifest file 'atropos.egg-info/SOURCES.txt' Copying atropos.egg-info to /<>/debian/atropos/usr/lib/python3.10/dist-packages/atropos-1.1.31.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/atropos/usr/bin copying build/scripts-3.10/atropos -> /<>/debian/atropos/usr/bin changing mode of /<>/debian/atropos/usr/bin/atropos to 755 debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install find debian -type d -name __pycache__ | xargs rm -rf find debian -type d -name tests | xargs rm -rf find debian -type f -name .adapters -delete make[1]: Leaving directory '/<>' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild debugedit: debian/atropos/usr/lib/python3/dist-packages/atropos/commands/trim/_qualtrim.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 74fa60be336ae2500a04dc76d20ec9628f67537d debugedit: debian/atropos/usr/lib/python3/dist-packages/atropos/align/_align.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 c09e602d429502e66ec88e704b1b172841ee699c debugedit: debian/atropos/usr/lib/python3/dist-packages/atropos/io/_seqio.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 8ee886c1301e80857be4d6752c8446eea9b55bbf dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package atropos: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package atropos: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing atropos-dbgsym (in debian/.debhelper/atropos/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing atropos (in debian/atropos); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/atropos/dbgsym-root/DEBIAN/control, package atropos-dbgsym, directory debian/.debhelper/atropos/dbgsym-root dpkg-deb: building package 'atropos-dbgsym' in 'debian/.debhelper/scratch-space/build-atropos/atropos-dbgsym_1.1.31+dfsg-3_riscv64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " Renaming atropos-dbgsym_1.1.31+dfsg-3_riscv64.deb to atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb pkgstripfiles: processing control file: debian/atropos/DEBIAN/control, package atropos, directory debian/atropos pkgstripfiles: Running PNG optimization (using 8 cpus) for package atropos ... pkgstripfiles: No PNG files. dpkg-deb: building package 'atropos' in '../atropos_1.1.31+dfsg-3_riscv64.deb'. dpkg-genbuildinfo --build=any -O../atropos_1.1.31+dfsg-3_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../atropos_1.1.31+dfsg-3_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-05-15T20:47:23Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ atropos_1.1.31+dfsg-3_riscv64.changes: -------------------------------------- Format: 1.8 Date: Mon, 04 Apr 2022 22:53:19 +0530 Source: atropos Binary: atropos Built-For-Profiles: noudeb Architecture: riscv64 Version: 1.1.31+dfsg-3 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: atropos - NGS read trimming tool that is specific, sensitive, and speedy Changes: atropos (1.1.31+dfsg-3) unstable; urgency=medium . * Team Upload. [ Mohammed Bilal ] * Initialize autopkgtest . [ Nilesh Patra ] * d/control: B-D on python3-all-dev instead of python3-dev in order to build extensions for all supported versions * d/t/control: Update test deps * d/t/run-unit-test: Do not test inplace, rather in AUTOPKGTEST_TMP Checksums-Sha1: 1ea102fee9767cddbd9de7951e9ee72929e994de 418580 atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb d8f7918c3593eacde57b9ba025c1eacdc22ccabb 8081 atropos_1.1.31+dfsg-3_riscv64.buildinfo efcdef4e6227815759fd7285d848b854da72e8af 192674 atropos_1.1.31+dfsg-3_riscv64.deb Checksums-Sha256: 6993b49dd71009283380782cc9952e69c2431e4bf89acee5af9fc7ed4c84a76e 418580 atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb a09c20425782ef01cf015b8b1309f9d52694c68f38a3921ea55f5735a316e1d8 8081 atropos_1.1.31+dfsg-3_riscv64.buildinfo a92bb653d72d87089722aa9b5a09457f1fffad2689c1b53eb77150c36bb3b88a 192674 atropos_1.1.31+dfsg-3_riscv64.deb Files: 0c1b6db03ae5809d6130c55f17a6d90b 418580 debug optional atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb 1db1aec2c221d52911e4ded4cfd5b08d 8081 science optional atropos_1.1.31+dfsg-3_riscv64.buildinfo c8ac0c47cebc5aa5f6649d5ed65cbeff 192674 science optional atropos_1.1.31+dfsg-3_riscv64.deb /<>/atropos_1.1.31+dfsg-3_riscv64.changes.new could not be renamed to /<>/atropos_1.1.31+dfsg-3_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: atropos Binary: atropos atropos-dbgsym Architecture: riscv64 Version: 1.1.31+dfsg-3 Checksums-Md5: 0c1b6db03ae5809d6130c55f17a6d90b 418580 atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb c8ac0c47cebc5aa5f6649d5ed65cbeff 192674 atropos_1.1.31+dfsg-3_riscv64.deb Checksums-Sha1: 1ea102fee9767cddbd9de7951e9ee72929e994de 418580 atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb efcdef4e6227815759fd7285d848b854da72e8af 192674 atropos_1.1.31+dfsg-3_riscv64.deb Checksums-Sha256: 6993b49dd71009283380782cc9952e69c2431e4bf89acee5af9fc7ed4c84a76e 418580 atropos-dbgsym_1.1.31+dfsg-3_riscv64.ddeb a92bb653d72d87089722aa9b5a09457f1fffad2689c1b53eb77150c36bb3b88a 192674 atropos_1.1.31+dfsg-3_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Sun, 15 May 2022 20:47:18 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-4ubuntu4), autotools-dev (= 20220109.1), base-files (= 12ubuntu5), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38-4ubuntu1), binutils-common (= 2.38-4ubuntu1), binutils-riscv64-linux-gnu (= 2.38-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-1ubuntu1), cython3 (= 0.29.28-1ubuntu3), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-python (= 5.20220403), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.7ubuntu3), dpkg-dev (= 1.21.7ubuntu3), dwz (= 0.14-1build2), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-1ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-1ubuntu1), gcc-11-base (= 11.3.0-1ubuntu1), gcc-12-base (= 12.1.0-2ubuntu1), gettext (= 0.21-4ubuntu4), gettext-base (= 0.21-4ubuntu4), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.62), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-1ubuntu1), libatomic1 (= 12.1.0-2ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38-4ubuntu1), libblkid1 (= 2.38-4ubuntu1), libbrotli1 (= 1.0.9-2build6), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build3), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.1.0-2ubuntu1), libcom-err2 (= 1.46.5-2ubuntu1), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38-4ubuntu1), libctf0 (= 2.38-4ubuntu1), libcurl3-gnutls (= 7.83.1-1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu3), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.7.1ubuntu1), libdeflate0 (= 1.10-2), libdpkg-perl (= 1.21.7ubuntu3), libdw1 (= 0.187-1), libelf1 (= 0.187-1), libexpat1 (= 2.4.8-1), libexpat1-dev (= 2.4.8-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-1ubuntu1), libgcc-s1 (= 12.1.0-2ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu3), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.4-2ubuntu1), libgomp1 (= 12.1.0-2ubuntu1), libgpg-error0 (= 1.45-2), libgssapi-krb5-2 (= 1.19.2-2), libhogweed6 (= 3.7.3-1build2), libhts3 (= 1.13+ds-2build2), libhtscodecs2 (= 1.2.1-1), libicu71 (= 71.1-3), libidn2-0 (= 2.3.2-2build1), libisl23 (= 0.24-2build1), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-sphinxdoc (= 4.5.0-3), libjs-underscore (= 1.13.3~dfsg+~1.11.4-1), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-2ubuntu3), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), libldap-2.5-0 (= 2.5.11+dfsg-1~exp1ubuntu3), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2ubuntu1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.7.3-1build2), libnghttp2-14 (= 1.47.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libpsl5 (= 0.21.0-1.2build2), libpython3-all-dev (= 3.10.4-0ubuntu2), libpython3-dev (= 3.10.4-0ubuntu2), libpython3-stdlib (= 3.10.4-0ubuntu2), libpython3.10 (= 3.10.4-4), libpython3.10-dev (= 3.10.4-4), libpython3.10-minimal (= 3.10.4-4), libpython3.10-stdlib (= 3.10.4-4), libreadline8 (= 8.1.2-1.2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.27+dfsg2-3ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg2-3ubuntu1), libselinux1 (= 3.3-1build2), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libsqlite3-0 (= 3.38.5-1), libssh-4 (= 0.9.6-2build1), libssl3 (= 3.0.3-0ubuntu1), libstdc++-11-dev (= 11.3.0-1ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.11-0ubuntu3.1), libtasn1-6 (= 4.18.0-4build1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-4), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu3.1), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-28.29), login (= 1:4.8.1-2ubuntu2), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 25), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3), media-types (= 8.0.0), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), po-debconf (= 1.0.21+nmu1), python-babel-localedata (= 2.8.0+dfsg.1-7), python3 (= 3.10.4-0ubuntu2), python3-all (= 3.10.4-0ubuntu2), python3-all-dev (= 3.10.4-0ubuntu2), python3-attr (= 21.2.0-1), python3-babel (= 2.8.0+dfsg.1-7), python3-colorama (= 0.4.4-1), python3-dev (= 3.10.4-0ubuntu2), python3-distutils (= 3.10.4-0ubuntu1), python3-iniconfig (= 1.1.1-2), python3-jinja2 (= 3.0.3-1), python3-lib2to3 (= 3.10.4-0ubuntu1), python3-loguru (= 0.6.0-1), python3-markupsafe (= 2.0.1-2build1), python3-minimal (= 3.10.4-0ubuntu2), python3-more-itertools (= 8.10.0-2), python3-packaging (= 21.3-1), python3-pkg-resources (= 59.6.0-1.2), python3-pluggy (= 1.0.0-1), python3-pokrok (= 0.2.0-2), python3-py (= 1.10.0-1), python3-pyparsing (= 3.0.7-2), python3-pysam (= 0.17.0+ds-2build1), python3-pytest (= 6.2.5-2ubuntu1), python3-setuptools (= 59.6.0-1.2), python3-setuptools-scm (= 6.4.2-1), python3-toml (= 0.10.2-1), python3-tomli (= 1.2.2-2), python3-tz (= 2022.1-1), python3-wheel (= 0.37.1-2), python3-xphyle (= 4.4.1-3), python3.10 (= 3.10.4-4), python3.10-dev (= 3.10.4-4), python3.10-minimal (= 3.10.4-4), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), tzdata (= 2022a-0ubuntu1), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1649092999" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ atropos_1.1.31+dfsg-3_riscv64.deb --------------------------------- new Debian package, version 2.0. size 192674 bytes: control archive=2996 bytes. 2275 bytes, 43 lines control 4301 bytes, 46 lines md5sums 265 bytes, 12 lines * postinst #!/bin/sh 409 bytes, 12 lines * prerm #!/bin/sh Package: atropos Version: 1.1.31+dfsg-3 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 753 Depends: libc6 (>= 2.27), cython3, python3 (<< 3.11), python3 (>= 3.10~), python3:any, python3-pysam Recommends: python3-jinja2 Section: science Priority: optional Homepage: https://github.com/jdidion/atropos Description: NGS read trimming tool that is specific, sensitive, and speedy Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer, with the primary improvements being: . 1. Multi-threading support, including an extremely fast "parallel write" mode. 2. Implementation of a new insert alignment-based trimming algorithm for paired-end reads that is substantially more sensitive and specific than the original Cutadapt adapter alignment-based algorithm. This algorithm can also correct mismatches between the overlapping portions of the reads. 3. Options for trimming specific types of data (miRNA, bisulfite-seq). 4. A new command ('detect') that will detect adapter sequences and other potential contaminants. 5. A new command ('error') that will estimate the sequencing error rate, which helps to select the appropriate adapter- and quality- trimming parameter values. 6. A new command ('qc') that generates read statistics similar to FastQC. The trim command can also compute read statistics both before and after trimming (using the '--stats' option). 7. Improved summary reports, including support for serialization formats (JSON, YAML, pickle), support for user-defined templates (via the optional Jinja2 dependency), and integration with MultiQC. 8. The ability to merge overlapping reads (this is experimental and the functionality is limited). 9. The ability to write the summary report and log messages to separate files. 10. The ability to read SAM/BAM files and read/write interleaved FASTQ files. 11. Direct trimming of reads from an SRA accession. 12. 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drwxr-xr-x root/root 0 2022-04-04 17:23 ./usr/share/ drwxr-xr-x root/root 0 2022-04-04 17:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-04-04 17:23 ./usr/share/doc/atropos/ -rw-r--r-- root/root 823 2022-04-04 17:23 ./usr/share/doc/atropos/changelog.Debian.gz -rw-r--r-- root/root 3955 2022-04-04 16:57 ./usr/share/doc/atropos/copyright drwxr-xr-x root/root 0 2022-04-04 17:23 ./usr/share/man/ drwxr-xr-x root/root 0 2022-04-04 17:23 ./usr/share/man/man1/ -rw-r--r-- root/root 1095 2022-04-04 17:23 ./usr/share/man/man1/atropos.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 21712 Build-Time: 312 Distribution: kinetic-proposed Host Architecture: riscv64 Install-Time: 434 Job: atropos_1.1.31+dfsg-3.dsc Machine Architecture: riscv64 Package: atropos Package-Time: 776 Source-Version: 1.1.31+dfsg-3 Space: 21712 Status: successful Version: 1.1.31+dfsg-3 -------------------------------------------------------------------------------- Finished at 2022-05-15T20:47:23Z Build needed 00:12:56, 21712k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 Scanning for processes to kill in build PACKAGEBUILD-23749370 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 Stopping target for build PACKAGEBUILD-23749370 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23749370 Removing build PACKAGEBUILD-23749370