0s autopkgtest [10:48:32]: starting date and time: 2024-11-13 10:48:32+0000 0s autopkgtest [10:48:32]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:48:32]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5vwc6psz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-bx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-5.secgroup --name adt-plucky-amd64-python-bx-20241113-104832-juju-7f2275-prod-proposed-migration-environment-15-6c7f5a81-7324-4d56-bed0-a42c491e5d6e --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 57s autopkgtest [10:49:29]: testbed dpkg architecture: amd64 57s autopkgtest [10:49:29]: testbed apt version: 2.9.8 57s autopkgtest [10:49:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 58s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 58s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 58s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 58s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 58s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 58s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 58s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 58s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 58s Fetched 2175 kB in 0s (5269 kB/s) 58s Reading package lists... 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 62s The following NEW packages will be installed: 62s python3.13-gdbm 62s The following packages will be upgraded: 62s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 62s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 253 kB of archives. 62s After this operation, 147 kB of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 62s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 62s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 62s Fetched 253 kB in 0s (7058 kB/s) 63s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 63s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 63s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 63s Setting up python3-minimal (3.12.7-1) ... 63s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 63s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 63s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 63s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 63s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 63s Selecting previously unselected package python3.13-gdbm. 63s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 63s Unpacking python3.13-gdbm (3.13.0-2) ... 63s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 63s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 63s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 63s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 63s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 63s Setting up python3.13-gdbm (3.13.0-2) ... 63s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 63s Setting up python3 (3.12.7-1) ... 64s Setting up python3-gdbm:amd64 (3.12.7-1) ... 64s Processing triggers for man-db (2.12.1-3) ... 64s Processing triggers for libc-bin (2.40-1ubuntu3) ... 64s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 65s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 67s Reading package lists... 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [10:49:42]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 71s autopkgtest [10:49:43]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bx 71s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-bx 0.13.0-1 (dsc) [2278 B] 71s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-bx 0.13.0-1 (tar) [1612 kB] 71s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-bx 0.13.0-1 (diff) [13.8 kB] 72s gpgv: Signature made Sun Sep 22 12:26:19 2024 UTC 72s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 72s gpgv: issuer "tchet@debian.org" 72s gpgv: Can't check signature: No public key 72s dpkg-source: warning: cannot verify inline signature for ./python-bx_0.13.0-1.dsc: no acceptable signature found 72s autopkgtest [10:49:44]: testing package python-bx version 0.13.0-1 72s autopkgtest [10:49:44]: build not needed 72s autopkgtest [10:49:44]: test pybuild-autopkgtest: preparing testbed 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Starting pkgProblemResolver with broken count: 0 75s Starting 2 pkgProblemResolver with broken count: 0 75s Done 75s The following additional packages will be installed: 75s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 75s cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper debugedit 75s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 75s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 75s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 75s libarchive-zip-perl libasan8 libblas3 libcc1-0 libdebhelper-perl 75s libexpat1-dev libfile-stripnondeterminism-perl libgcc-14-dev libgfortran5 75s libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc 75s libjs-underscore liblapack3 liblsan0 libmpc3 libpython3-all-dev 75s libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev 75s libpython3.13-minimal libpython3.13-stdlib libquadmath0 libstdc++-14-dev 75s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 75s pybuild-plugin-pyproject python3-all python3-all-dev python3-build 75s python3-bx python3-dev python3-iniconfig python3-installer python3-lzo 75s python3-numpy python3-packaging python3-pluggy python3-pyproject-hooks 75s python3-pytest python3-pytest-cython python3-toml python3-wheel 75s python3.12-dev python3.13 python3.13-dev python3.13-minimal zlib1g-dev 75s Suggested packages: 75s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 75s cpp-14-doc cython-doc dh-make flit g++-multilib g++-14-multilib gcc-14-doc 75s gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-14-multilib 75s gdb-x86-64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 75s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 75s libmail-box-perl python3-pip python3-venv python-build-doc 75s python-installer-doc gfortran python-numpy-doc python3.13-venv 75s python3.13-doc binfmt-support 75s Recommended packages: 75s libarchive-cpio-perl javascript-common libltdl-dev libmail-sendmail-perl 76s The following NEW packages will be installed: 76s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 76s cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper 76s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 76s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 76s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 76s libarchive-zip-perl libasan8 libblas3 libcc1-0 libdebhelper-perl 76s libexpat1-dev libfile-stripnondeterminism-perl libgcc-14-dev libgfortran5 76s libgomp1 libhwasan0 libisl23 libitm1 libjs-jquery libjs-sphinxdoc 76s libjs-underscore liblapack3 liblsan0 libmpc3 libpython3-all-dev 76s libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev 76s libpython3.13-minimal libpython3.13-stdlib libquadmath0 libstdc++-14-dev 76s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 76s pybuild-plugin-pyproject python3-all python3-all-dev python3-build 76s python3-bx python3-dev python3-iniconfig python3-installer python3-lzo 76s python3-numpy python3-packaging python3-pluggy python3-pyproject-hooks 76s python3-pytest python3-pytest-cython python3-toml python3-wheel 76s python3.12-dev python3.13 python3.13-dev python3.13-minimal zlib1g-dev 76s 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 104 MB/104 MB of archives. 76s After this operation, 379 MB of additional disk space will be used. 76s Get:1 /tmp/autopkgtest.crjIka/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [836 B] 76s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 76s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 76s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 76s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 76s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 76s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 76s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 76s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 76s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 76s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 76s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 76s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 76s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 76s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 76s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 76s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 76s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 76s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 76s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 76s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 76s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 76s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 76s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 76s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 76s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 76s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 76s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-1ubuntu1 [2491 kB] 76s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 76s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 76s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 76s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 76s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 76s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 76s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 76s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 76s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 76s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 76s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 76s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 76s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 76s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 76s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.2-2 [140 kB] 76s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 76s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 76s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 76s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 76s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 76s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 76s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB] 76s Get:58 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-dev amd64 3.12.7-1 [10.3 kB] 76s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 77s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.0-2 [2321 kB] 77s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.0-2 [5488 kB] 77s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-all-dev amd64 3.12.7-1 [916 B] 77s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 77s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 77s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 77s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 77s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.44.0-1 [54.2 kB] 77s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 77s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 77s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 77s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 77s Get:72 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 77s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] 77s Get:74 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-dev amd64 3.12.7-1 [26.7 kB] 77s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.0-2 [507 kB] 77s Get:76 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all-dev amd64 3.12.7-1 [914 B] 77s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lzo amd64 1.15-2 [8928 B] 77s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 77s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bx amd64 0.13.0-1 [811 kB] 77s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 77s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 77s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 77s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-cython all 0.3.1-1 [7270 B] 77s Fetched 104 MB in 1s (103 MB/s) 77s Selecting previously unselected package libpython3.13-minimal:amd64. 77s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75548 files and directories currently installed.) 77s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 77s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 77s Selecting previously unselected package python3.13-minimal. 77s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 77s Unpacking python3.13-minimal (3.13.0-2) ... 77s Selecting previously unselected package m4. 77s Preparing to unpack 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to unpack .../19-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 78s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 78s Selecting previously unselected package libhwasan0:amd64. 78s Preparing to unpack .../20-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 78s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 79s Selecting previously unselected package libquadmath0:amd64. 79s Preparing to unpack .../21-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 79s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 79s Selecting previously unselected package libgcc-14-dev:amd64. 79s Preparing to unpack .../22-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 79s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 79s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 79s Preparing to unpack .../23-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 79s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 79s Selecting previously unselected package gcc-14. 79s Preparing to unpack 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package libtool. 80s Preparing to unpack .../35-libtool_2.4.7-7build1_all.deb ... 80s Unpacking libtool (2.4.7-7build1) ... 80s Selecting previously unselected package dh-autoreconf. 80s Preparing to unpack .../36-dh-autoreconf_20_all.deb ... 80s Unpacking dh-autoreconf (20) ... 80s Selecting previously unselected package libarchive-zip-perl. 80s Preparing to unpack .../37-libarchive-zip-perl_1.68-1_all.deb ... 80s Unpacking libarchive-zip-perl (1.68-1) ... 80s Selecting previously unselected package libfile-stripnondeterminism-perl. 80s Preparing to unpack .../38-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 80s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 80s Selecting previously unselected package dh-strip-nondeterminism. 80s Preparing to unpack .../39-dh-strip-nondeterminism_1.14.0-1_all.deb ... 80s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 80s Selecting previously unselected package debugedit. 80s Preparing to unpack .../40-debugedit_1%3a5.1-1_amd64.deb 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dh-python (6.20241024) ... 81s Selecting previously unselected package libblas3:amd64. 81s Preparing to unpack .../47-libblas3_3.12.0-3build2_amd64.deb ... 81s Unpacking libblas3:amd64 (3.12.0-3build2) ... 81s Selecting previously unselected package libexpat1-dev:amd64. 81s Preparing to unpack .../48-libexpat1-dev_2.6.2-2_amd64.deb ... 81s Unpacking libexpat1-dev:amd64 (2.6.2-2) ... 81s Selecting previously unselected package libgfortran5:amd64. 81s Preparing to unpack .../49-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 81s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 81s Selecting previously unselected package libjs-jquery. 81s Preparing to unpack .../50-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 81s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 81s Selecting previously unselected package libjs-underscore. 81s Preparing to unpack .../51-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 81s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 81s Selecting previously unselected package libjs-sphinxdoc. 81s Preparing to unpack .../52-libjs-sphinxdoc_7.4.7-4_all.deb ... 81s Unpacking libjs-sphinxdoc (7.4.7-4) ... 81s Selecting previously unselected package liblapack3:amd64. 81s Preparing to unpack .../53-liblapack3_3.12.0-3build2_amd64.deb ... 81s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 81s Selecting previously unselected package zlib1g-dev:amd64. 81s Preparing to unpack .../54-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 81s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 81s Selecting previously unselected package libpython3.12-dev:amd64. 81s Preparing to unpack .../55-libpython3.12-dev_3.12.7-3_amd64.deb ... 81s Unpacking libpython3.12-dev:amd64 (3.12.7-3) ... 81s Selecting previously unselected package libpython3-dev:amd64. 81s Preparing to unpack .../56-libpython3-dev_3.12.7-1_amd64.deb ... 81s Unpacking libpython3-dev:amd64 (3.12.7-1) ... 81s Selecting previously unselected package 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Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 84s Setting up autotools-dev (20220109.1) ... 84s Setting up libblas3:amd64 (3.12.0-3build2) ... 84s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 84s Setting up python3-packaging (24.1-1) ... 84s Setting up libexpat1-dev:amd64 (2.6.2-2) ... 84s Setting up python3-pyproject-hooks (1.2.0-1) ... 84s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 84s Setting up libmpc3:amd64 (1.3.1-1build2) ... 84s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ... 86s Setting up autopoint (0.22.5-2) ... 86s Setting up python3-toml (0.10.2-1) ... 86s Setting up python3-installer (0.7.0+dfsg1-3) ... 86s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 86s Setting up autoconf (2.72-3) ... 86s Setting up python3-pluggy (1.5.0-1) ... 86s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 86s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 86s Setting up dwz (0.15-1build6) ... 86s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 86s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 86s Setting up debugedit (1:5.1-1) ... 86s Setting up python3.13-minimal (3.13.0-2) ... 88s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 88s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 88s Setting up libisl23:amd64 (0.27-1) ... 88s Setting up python3-build (1.2.2-1) ... 88s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 88s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 88s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 88s Setting up python3-lzo:amd64 (1.15-2) ... 88s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 88s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 88s Setting up libpython3.13:amd64 (3.13.0-2) ... 88s Setting up automake (1:1.16.5-1.3ubuntu1) ... 88s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 88s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 88s Setting up liblapack3:amd64 (3.12.0-3build2) ... 88s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 88s Setting up gettext (0.22.5-2) ... 88s Setting up python3.13 (3.13.0-2) ... 89s Setting up pybuild-plugin-pyproject (6.20241024) ... 89s Setting up python3-pytest (8.3.3-1) ... 90s Setting up python3-all (3.12.7-1) ... 90s Setting up libpython3.12-dev:amd64 (3.12.7-3) ... 90s Setting up intltool-debian (0.35.0+20060710.6) ... 90s Setting up libpython3.13-dev:amd64 (3.13.0-2) ... 90s Setting up python3.12-dev (3.12.7-3) ... 90s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 90s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 94s Setting up libjs-sphinxdoc (7.4.7-4) ... 94s Setting up cpp-14 (14.2.0-8ubuntu1) ... 94s Setting up dh-strip-nondeterminism (1.14.0-1) ... 94s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 94s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 94s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 94s Setting up python3-bx (0.13.0-1) ... 94s Setting up libpython3-dev:amd64 (3.12.7-1) ... 94s Setting up python3-pytest-cython (0.3.1-1) ... 95s Setting up python3.13-dev (3.13.0-2) ... 95s Setting up po-debconf (1.0.21+nmu1) ... 95s Setting up libpython3-all-dev:amd64 (3.12.7-1) ... 95s Setting up python3-dev (3.12.7-1) ... 95s Setting up cpp (4:14.1.0-2ubuntu1) ... 95s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 95s Setting up python3-all-dev (3.12.7-1) ... 95s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 95s Setting up gcc-14 (14.2.0-8ubuntu1) ... 95s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 95s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 95s Setting up g++-14 (14.2.0-8ubuntu1) ... 95s Setting up libtool (2.4.7-7build1) ... 95s Setting up gcc (4:14.1.0-2ubuntu1) ... 95s Setting up dh-autoreconf (20) ... 95s Setting up g++ (4:14.1.0-2ubuntu1) ... 95s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 95s Setting up build-essential (12.10ubuntu1) ... 95s Setting up debhelper (13.20ubuntu1) ... 95s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 95s Setting up autopkgtest-satdep (0) ... 95s Processing triggers for systemd (256.5-2ubuntu4) ... 95s Processing triggers for man-db (2.12.1-3) ... 96s Processing triggers for install-info (7.1.1-1) ... 96s Processing triggers for libc-bin (2.40-1ubuntu3) ... 100s (Reading database ... 81202 files and directories currently installed.) 100s Removing autopkgtest-satdep (0) ... 100s autopkgtest [10:50:12]: test pybuild-autopkgtest: pybuild-autopkgtest 100s autopkgtest [10:50:12]: test pybuild-autopkgtest: [----------------------- 101s find lib -name "*_tests.py" >> debian/pybuild.testfiles 101s pybuild-autopkgtest 101s I: pybuild base:311: cd /tmp/autopkgtest.crjIka/autopkgtest_tmp/build; python3.13 -m pytest 103s ============================= test session starts ============================== 103s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 103s rootdir: /tmp/autopkgtest.crjIka/autopkgtest_tmp/build 103s configfile: pytest.ini 103s plugins: cython-0.3.1, typeguard-4.4.1 103s collected 22 items / 44 errors 103s 103s ==================================== ERRORS ==================================== 103s _____________________ ERROR collecting array_tree_tests.py _____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/array_tree_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s array_tree_tests.py:11: in 103s from bx.arrays.array_tree import ( 103s E ModuleNotFoundError: No module named 'bx.arrays.array_tree' 103s _____________________ ERROR collecting array_tree_tests.py _____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/array_tree_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s array_tree_tests.py:11: in 103s from bx.arrays.array_tree import ( 103s E ModuleNotFoundError: No module named 'bx.arrays.array_tree' 103s ________________________ ERROR collecting bgzf_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/bgzf_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s bgzf_tests.py:1: in 103s import bx.misc.bgzf 103s E ModuleNotFoundError: No module named 'bx.misc.bgzf' 103s ________________________ ERROR collecting bgzf_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/bgzf_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s bgzf_tests.py:1: in 103s import bx.misc.bgzf 103s E ModuleNotFoundError: No module named 'bx.misc.bgzf' 103s _______________________ ERROR collecting bigwig_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/bigwig_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s bigwig_tests.py:4: in 103s import numpy 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _______________________ ERROR collecting bigwig_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/bigwig_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s bigwig_tests.py:4: in 103s import numpy 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ____________________ ERROR collecting binned_array_tests.py ____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/binned_array_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s binned_array_tests.py:6: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ____________________ ERROR collecting binned_array_tests.py ____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/binned_array_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s binned_array_tests.py:6: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _______________________ ERROR collecting bitset_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/bitset_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s bitset_tests.py:7: in 103s import bx.bitset 103s E ModuleNotFoundError: No module named 'bx.bitset' 103s _______________________ ERROR collecting bitset_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/bitset_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s bitset_tests.py:7: in 103s import bx.bitset 103s E ModuleNotFoundError: No module named 'bx.bitset' 103s ________________________ ERROR collecting cdb_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/cdb_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s cdb_tests.py:3: in 103s from bx.misc.cdb import FileCDBDict 103s /usr/lib/python3/dist-packages/bx/misc/cdb.py:4: in 103s from bx.misc.binary_file import ( 103s /usr/lib/python3/dist-packages/bx/misc/binary_file.py:8: in 103s import numpy 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ________________________ ERROR collecting cdb_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/cdb_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s cdb_tests.py:3: in 103s from bx.misc.cdb import FileCDBDict 103s /usr/lib/python3/dist-packages/bx/misc/cdb.py:4: in 103s from bx.misc.binary_file import ( 103s /usr/lib/python3/dist-packages/bx/misc/binary_file.py:8: in 103s import numpy 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ______________________ ERROR collecting cluster_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/cluster_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s cluster_tests.py:3: in 103s from bx.intervals.cluster import ClusterTree 103s /usr/lib/python3/dist-packages/bx/intervals/__init__.py:7: in 103s from bx.intervals.intersection import ( 103s E ModuleNotFoundError: No module named 'bx.intervals.intersection' 103s ______________________ ERROR collecting cluster_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/cluster_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s cluster_tests.py:3: in 103s from bx.intervals.cluster import ClusterTree 103s /usr/lib/python3/dist-packages/bx/intervals/__init__.py:7: in 103s from bx.intervals.intersection import ( 103s E ModuleNotFoundError: No module named 'bx.intervals.intersection' 103s ________________________ ERROR collecting epo_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/epo_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s epo_tests.py:7: in 103s import numpy as np 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ________________________ ERROR collecting epo_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/epo_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s epo_tests.py:7: in 103s import numpy as np 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _______________________ ERROR collecting fasta_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/fasta_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s fasta_tests.py:7: in 103s from bx.seq import fasta 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s _______________________ ERROR collecting fasta_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/fasta_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s fasta_tests.py:7: in 103s from bx.seq import fasta 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s ____________________ ERROR collecting intersection_tests.py ____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/intersection_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s intersection_tests.py:10: in 103s from bx.intervals.intersection import ( 103s /usr/lib/python3/dist-packages/bx/intervals/__init__.py:7: in 103s from bx.intervals.intersection import ( 103s E ModuleNotFoundError: No module named 'bx.intervals.intersection' 103s ____________________ ERROR collecting intersection_tests.py ____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/intersection_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s intersection_tests.py:10: in 103s from bx.intervals.intersection import ( 103s /usr/lib/python3/dist-packages/bx/intervals/__init__.py:7: in 103s from bx.intervals.intersection import ( 103s E ModuleNotFoundError: No module named 'bx.intervals.intersection' 103s ________________________ ERROR collecting lav_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/lav_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s lav_tests.py:7: in 103s import bx.align.lav as lav 103s /usr/lib/python3/dist-packages/bx/align/lav.py:11: in 103s import bx.seq 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s ________________________ ERROR collecting lav_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/lav_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s lav_tests.py:7: in 103s import bx.align.lav as lav 103s /usr/lib/python3/dist-packages/bx/align/lav.py:11: in 103s import bx.seq 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s ________________________ ERROR collecting nib_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/nib_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s nib_tests.py:7: in 103s from bx.seq import nib 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s ________________________ ERROR collecting nib_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/nib_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s nib_tests.py:7: in 103s from bx.seq import nib 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s _______________________ ERROR collecting phast_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/phast_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s phast_tests.py:7: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _______________________ ERROR collecting phast_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/phast_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s phast_tests.py:7: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ________________________ ERROR collecting pwm_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/pwm_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s pwm_tests.py:4: in 103s import bx.pwm.position_weight_matrix as pwm 103s /usr/lib/python3/dist-packages/bx/pwm/position_weight_matrix.py:6: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ________________________ ERROR collecting pwm_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/pwm_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s pwm_tests.py:4: in 103s import bx.pwm.position_weight_matrix as pwm 103s /usr/lib/python3/dist-packages/bx/pwm/position_weight_matrix.py:6: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ________________________ ERROR collecting qdna_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/qdna_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s qdna_tests.py:7: in 103s from bx.seq import qdna 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s ________________________ ERROR collecting qdna_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/qdna_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s qdna_tests.py:7: in 103s from bx.seq import qdna 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s _______________________ ERROR collecting score_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/score_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s score_tests.py:8: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _______________________ ERROR collecting score_tests.py ________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/score_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s score_tests.py:8: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _____________________ ERROR collecting seekbzip2_tests.py ______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/seekbzip2_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s seekbzip2_tests.py:10: in 103s from bx.misc import seekbzip2 103s /usr/lib/python3/dist-packages/bx/misc/seekbzip2.py:7: in 103s from ._seekbzip2 import SeekBzip2 103s E ModuleNotFoundError: No module named 'bx.misc._seekbzip2' 103s _____________________ ERROR collecting seekbzip2_tests.py ______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/seekbzip2_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s seekbzip2_tests.py:10: in 103s from bx.misc import seekbzip2 103s /usr/lib/python3/dist-packages/bx/misc/seekbzip2.py:7: in 103s from ._seekbzip2 import SeekBzip2 103s E ModuleNotFoundError: No module named 'bx.misc._seekbzip2' 103s ________________________ ERROR collecting seq_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/seq_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s seq_tests.py:7: in 103s import bx.seq 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s ________________________ ERROR collecting seq_tests.py _________________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/seq_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s seq_tests.py:7: in 103s import bx.seq 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s _____________________ ERROR collecting seqmapping_tests.py _____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/seqmapping_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s seqmapping_tests.py:8: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _____________________ ERROR collecting seqmapping_tests.py _____________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/seqmapping_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s seqmapping_tests.py:8: in 103s from numpy import ( 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ______________________ ERROR collecting sitemask_tests.py ______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/sitemask_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s sitemask_tests.py:9: in 103s from bx.align.sitemask import cpg 103s /usr/lib/python3/dist-packages/bx/align/sitemask/cpg.py:6: in 103s from ._cpg import ( 103s E ModuleNotFoundError: No module named 'bx.align.sitemask._cpg' 103s ______________________ ERROR collecting sitemask_tests.py ______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/sitemask_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s sitemask_tests.py:9: in 103s from bx.align.sitemask import cpg 103s /usr/lib/python3/dist-packages/bx/align/sitemask/cpg.py:6: in 103s from ._cpg import ( 103s E ModuleNotFoundError: No module named 'bx.align.sitemask._cpg' 103s ______________________ ERROR collecting transfac_tests.py ______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/transfac_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s transfac_tests.py:3: in 103s from numpy import allclose 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s ______________________ ERROR collecting transfac_tests.py ______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/transfac_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 103s from . import multiarray 103s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 103s from . import overrides 103s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 103s from numpy.core._multiarray_umath import ( 103s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 103s 103s During handling of the above exception, another exception occurred: 103s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 103s from numpy.__config__ import show as show_config 103s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 103s from numpy.core._multiarray_umath import ( 103s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 103s raise ImportError(msg) 103s E ImportError: 103s E 103s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 103s E 103s E Importing the numpy C-extensions failed. This error can happen for 103s E many reasons, often due to issues with your setup or how NumPy was 103s E installed. 103s E 103s E We have compiled some common reasons and troubleshooting tips at: 103s E 103s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 103s E 103s E Please note and check the following: 103s E 103s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 103s E * The NumPy version is: "1.26.4" 103s E 103s E and make sure that they are the versions you expect. 103s E Please carefully study the documentation linked above for further help. 103s E 103s E Original error was: No module named 'numpy.core._multiarray_umath' 103s 103s The above exception was the direct cause of the following exception: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s transfac_tests.py:3: in 103s from numpy import allclose 103s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 103s raise ImportError(msg) from e 103s E ImportError: Error importing numpy: you should not try to import numpy from 103s E its source directory; please exit the numpy source tree, and relaunch 103s E your python interpreter from there. 103s _______________________ ERROR collecting twobit_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/twobit_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s twobit_tests.py:5: in 103s from bx.seq import twobit 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s _______________________ ERROR collecting twobit_tests.py _______________________ 103s ImportError while importing test module '/tmp/autopkgtest.crjIka/autopkgtest_tmp/build/twobit_tests.py'. 103s Hint: make sure your test modules/packages have valid Python names. 103s Traceback: 103s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 103s return _bootstrap._gcd_import(name[level:], package, level) 103s twobit_tests.py:5: in 103s from bx.seq import twobit 103s /usr/lib/python3/dist-packages/bx/seq/__init__.py:7: in 103s from bx.seq.core import ( 103s /usr/lib/python3/dist-packages/bx/seq/core.py:11: in 103s from . import ( 103s /usr/lib/python3/dist-packages/bx/seq/nib.py:30: in 103s from . import _nib 103s E ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/usr/lib/python3/dist-packages/bx/seq/__init__.py) 103s =============================== warnings summary =============================== 103s ../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500 103s /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. 103s self.args, self.args_source = self._decide_args( 103s 103s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 103s =========================== short test summary info ============================ 103s ERROR array_tree_tests.py 103s ERROR array_tree_tests.py 103s ERROR bgzf_tests.py 103s ERROR bgzf_tests.py 103s ERROR bigwig_tests.py 103s ERROR bigwig_tests.py 103s ERROR binned_array_tests.py 103s ERROR binned_array_tests.py 103s ERROR bitset_tests.py 103s ERROR bitset_tests.py 103s ERROR cdb_tests.py 103s ERROR cdb_tests.py 103s ERROR cluster_tests.py 103s ERROR cluster_tests.py 103s ERROR epo_tests.py 103s ERROR epo_tests.py 103s ERROR fasta_tests.py 103s ERROR fasta_tests.py 103s ERROR intersection_tests.py 103s ERROR intersection_tests.py 103s ERROR lav_tests.py 103s ERROR lav_tests.py 103s ERROR nib_tests.py 103s ERROR nib_tests.py 103s ERROR phast_tests.py 103s ERROR phast_tests.py 103s ERROR pwm_tests.py 103s ERROR pwm_tests.py 103s ERROR qdna_tests.py 103s ERROR qdna_tests.py 103s ERROR score_tests.py 103s ERROR score_tests.py 103s ERROR seekbzip2_tests.py 103s ERROR seekbzip2_tests.py 103s ERROR seq_tests.py 103s ERROR seq_tests.py 103s ERROR seqmapping_tests.py 103s ERROR seqmapping_tests.py 103s ERROR sitemask_tests.py 103s ERROR sitemask_tests.py 103s ERROR transfac_tests.py 103s ERROR transfac_tests.py 103s ERROR twobit_tests.py 103s ERROR twobit_tests.py 103s !!!!!!!!!!!!!!!!!!! Interrupted: 44 errors during collection !!!!!!!!!!!!!!!!!!! 103s ======================== 1 warning, 44 errors in 1.16s ========================= 103s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.crjIka/autopkgtest_tmp/build; python3.13 -m pytest 103s I: pybuild base:311: cd /tmp/autopkgtest.crjIka/autopkgtest_tmp/build; python3.12 -m pytest 103s ============================= test session starts ============================== 103s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 103s rootdir: /tmp/autopkgtest.crjIka/autopkgtest_tmp/build 103s configfile: pytest.ini 103s plugins: cython-0.3.1, typeguard-4.4.1 103s collected 132 items 103s 105s array_tree_tests.py ...... [ 4%] 105s bgzf_tests.py . [ 5%] 105s bigwig_tests.py ........................... [ 25%] 106s binned_array_tests.py .... [ 28%] 106s bitset_tests.py .................. [ 42%] 106s cdb_tests.py . [ 43%] 106s cluster_tests.py ............. [ 53%] 106s epo_tests.py ..... [ 56%] 106s fasta_tests.py . [ 57%] 106s fpconst_tests.py . [ 58%] 107s intersection_tests.py ............. [ 68%] 108s interval_index_file_tests.py ... [ 70%] 108s lav_tests.py . [ 71%] 108s maf_tests.py ........ [ 77%] 108s newick_tests.py ........ [ 83%] 108s nib_tests.py . [ 84%] 108s phast_tests.py . [ 84%] 108s pwm_tests.py . [ 85%] 108s qdna_tests.py . [ 86%] 108s score_tests.py ..... [ 90%] 108s seq_tests.py .... [ 93%] 108s sitemask_tests.py ... [ 95%] 108s transfac_tests.py . [ 96%] 108s twobit_tests.py ... [ 98%] 108s wiggle_tests.py .. [100%] 108s 108s =============================== warnings summary =============================== 108s ../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500 108s /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. 108s self.args, self.args_source = self._decide_args( 108s 108s bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 12000 10 mean n/a n/a n/a n/a -0.164968 -0.194169 -0.0533029 0.00390226 -0.00226906 -0.0365958\n] 108s bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 20000 100 mean n/a n/a n/a n/a n/a n/a n/a n/a n/a -0.163546 -0.272118 -0.127111 -0.116169 0.0202627 -0.0243522 0.0349913 -0.0054408 -0.00101548 -0.0307148 -0.0374406 -0.0024669 -0.034042 -0.0343892 -0.0199075 -0.0406878 -0.0322236 -0.080479 -0.235991 -0.0897865 -0.041593 0.019942 -0.0608448 0.0144338 -0.0348468 0.0195101 -0.0555526 -0.0892809 0.011672 -0.173894 -0.0849444 0.0718796 0.0608432 0.0313183 0.0439315 -0.0242363 0.03288 0.0318241 0.122005 0.0879138 0.00102565 0.0334753 -0.00263047 -0.103023 -0.0275437 0.0958326 0.0147229 -0.0629772 0.00541821 0.062474 0.069069 -0.0389339 0.0206174 0.0278476 -0.0182009 0.00568736 0.000397305 0.13104 0.105984 -0.00662042 0.143469 0.111045 0.0322849 0.11452 0.0865186 0.055436 0.141388 0.103004 -0.00350213 0.053879 0.10582 0.0983312 -0.0351239 0.10085 0.110439 0.0451646 -0.00949231 0.0487825 0.042197 -0.00328549 -0.00851082 -0.0437525 0.0618735 -0.0315407 -0.00756448 -0.0523631 0.0432315 0.0228745 0.106009 0.0299314 0.0473805\n] 108s bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 12000 100 mean n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 0.0508425 0.0508425 -0.0768488 -0.189129 -0.439008 -0.182524 -0.304712 -0.197935 -0.462124 -0.194633 -0.2882 -0.0570346 -0.0724456 -0.301409 0.0508425 -0.0702441 -0.182524 0.0508425 0.0508425 -0.55459 0.0508425 0.0508425 0.0508425 0.0508425 0.00460946 -0.0152047 -0.0152047 -0.095562 -0.0570346 0.0695559 0.127898 0.000206554 -0.013003 0.0167182 -0.0559341 0.0508425 0.0904709 0.101479 -0.155005 -0.0812521 0.0145168 0.0992772 0.10368 -0.155005 0.002408 -0.0911592 -0.0768488 0.013416 -0.00529754 -0.0702443 0.0013071 -0.0702442 0.0919354 -0.101144 -0.000301097\n] 108s bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 20000 1000 mean n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 0.0508425 0.0508425 0.0508425 0.0112142 -0.164912 -0.206742 -0.171516 -0.671274 -0.206741 -0.415891 0.0508425 -0.411489 -0.197936 0.0508425 -0.446713 -0.219951 -0.704298 -0.200137 -0.189129 -0.41369 -0.162711 0.0508425 -0.164912 -0.195734 0.0508425 -0.440108 -0.162711 0.0508425 0.0508425 0.0508425 -0.191331 -0.200137 -0.164912 0.0508425 0.0508425 0.0508425 0.0508425 -0.909043 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python{version} -p "3.13 3.12" returned exit code 13 108s make: *** [/tmp/mcGbyyyxF8/run:4: pybuild-autopkgtest] Error 25 108s pybuild-autopkgtest: error: /tmp/mcGbyyyxF8/run pybuild-autopkgtest returned exit code 2 109s autopkgtest [10:50:21]: test pybuild-autopkgtest: -----------------------] 109s autopkgtest [10:50:21]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 109s pybuild-autopkgtest FAIL non-zero exit status 25 109s autopkgtest [10:50:21]: @@@@@@@@@@@@@@@@@@@@ summary 109s pybuild-autopkgtest FAIL non-zero exit status 25 121s nova [W] Skipping flock for amd64 121s Creating nova instance adt-plucky-amd64-python-bx-20241113-104832-juju-7f2275-prod-proposed-migration-environment-15-6c7f5a81-7324-4d56-bed0-a42c491e5d6e from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...