0s autopkgtest [17:23:39]: starting date and time: 2024-03-24 17:23:39+0000 0s autopkgtest [17:23:39]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:23:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._huzibwf/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:python-pysam,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade python-pybedtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-17.secgroup --name adt-noble-arm64-python-pybedtools-20240324-170914-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 91s autopkgtest [17:25:10]: testbed dpkg architecture: arm64 91s autopkgtest [17:25:10]: testbed apt version: 2.7.12 91s autopkgtest [17:25:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 92s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 92s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 93s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 93s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 93s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 93s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 93s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 93s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 93s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 93s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 93s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 93s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 95s Fetched 9850 kB in 2s (5327 kB/s) 96s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 100s The following packages will be REMOVED: 100s libssl3 100s The following NEW packages will be installed: 100s libssl3t64 100s The following packages have been kept back: 100s curl 100s The following packages will be upgraded: 100s openssl 100s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 100s Need to get 2777 kB of archives. 100s After this operation, 139 kB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 101s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 102s Fetched 2777 kB in 2s (1398 kB/s) 102s (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 ... 75911 files and directories currently installed.) 102s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 102s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 102s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 102s wget depends on libssl3 (>= 3.0.0). 102s u-boot-tools depends on libssl3 (>= 3.0.0). 102s tnftp depends on libssl3 (>= 3.0.0). 102s tcpdump depends on libssl3 (>= 3.0.0). 102s systemd-resolved depends on libssl3 (>= 3.0.0). 102s systemd depends on libssl3 (>= 3.0.0). 102s sudo depends on libssl3 (>= 3.0.0). 102s sbsigntool depends on libssl3 (>= 3.0.0). 102s rsync depends on libssl3 (>= 3.0.0). 102s python3-cryptography depends on libssl3 (>= 3.0.0). 102s openssh-server depends on libssl3 (>= 3.0.10). 102s openssh-client depends on libssl3 (>= 3.0.10). 102s mtd-utils depends on libssl3 (>= 3.0.0). 102s mokutil depends on libssl3 (>= 3.0.0). 102s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 102s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 102s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 102s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 102s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 102s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 102s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 102s libnvme1 depends on libssl3 (>= 3.0.0). 102s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 102s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 102s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 102s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 102s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 102s kmod depends on libssl3 (>= 3.0.0). 102s dhcpcd-base depends on libssl3 (>= 3.0.0). 102s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 102s 102s (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 ... 75911 files and directories currently installed.) 102s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 102s Selecting previously unselected package libssl3t64:arm64. 102s (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 ... 75900 files and directories currently installed.) 102s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 102s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 102s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 102s Setting up openssl (3.0.13-0ubuntu2) ... 102s Processing triggers for man-db (2.12.0-3) ... 103s Processing triggers for libc-bin (2.39-0ubuntu6) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 105s sh: Attempting to set up Debian/Ubuntu apt sources automatically 105s sh: Distribution appears to be Ubuntu 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s eatmydata is already the newest version (131-1). 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s dbus is already the newest version (1.14.10-4ubuntu1). 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s rng-tools-debian is already the newest version (2.4). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s The following packages will be REMOVED: 109s cloud-init* python3-configobj* python3-debconf* 109s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 109s After this operation, 3256 kB disk space will be freed. 109s (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 ... 75913 files and directories currently installed.) 109s Removing cloud-init (24.1.2-0ubuntu1) ... 110s Removing python3-configobj (5.0.8-3) ... 110s Removing python3-debconf (1.5.86) ... 110s Processing triggers for man-db (2.12.0-3) ... 110s (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 ... 75524 files and directories currently installed.) 110s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 111s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 111s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 111s invoke-rc.d: policy-rc.d denied execution of try-restart. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s linux-generic is already the newest version (6.8.0-11.11+1). 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 112s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 112s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 114s Reading package lists... 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s autopkgtest [17:25:36]: rebooting testbed after setup commands that affected boot 153s autopkgtest [17:26:12]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 156s autopkgtest [17:26:15]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pybedtools 162s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-pybedtools 0.9.1-1 (dsc) [2520 B] 162s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-pybedtools 0.9.1-1 (tar) [12.0 MB] 162s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-pybedtools 0.9.1-1 (diff) [29.9 kB] 162s gpgv: Signature made Wed Nov 1 06:51:36 2023 UTC 162s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 162s gpgv: issuer "tille@debian.org" 162s gpgv: Can't check signature: No public key 162s dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.9.1-1.dsc: no acceptable signature found 162s autopkgtest [17:26:21]: testing package python-pybedtools version 0.9.1-1 162s autopkgtest [17:26:21]: build not needed 163s autopkgtest [17:26:22]: test autodep8-python3: preparing testbed 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Starting pkgProblemResolver with broken count: 0 172s Starting 2 pkgProblemResolver with broken count: 0 172s Done 173s The following additional packages will be installed: 173s libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 liblapack3 173s python3-all python3-numpy python3-pybedtools python3-pysam 173s Suggested packages: 173s gcc gfortran python3-dev python3-pytest python-pybedtools-doc 173s The following NEW packages will be installed: 173s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 173s liblapack3 python3-all python3-numpy python3-pybedtools python3-pysam 173s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 24.6 MB/24.6 MB of archives. 173s After this operation, 95.2 MB of additional disk space will be used. 173s Get:1 /tmp/autopkgtest.5URAbJ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 173s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 173s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 173s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 173s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 173s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 173s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 174s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 174s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 174s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 175s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybedtools arm64 0.9.1-1 [12.3 MB] 176s Fetched 24.6 MB in 3s (9316 kB/s) 176s Selecting previously unselected package libblas3:arm64. 176s (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 ... 75469 files and directories currently installed.) 176s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ... 176s Unpacking libblas3:arm64 (3.12.0-3) ... 176s Selecting previously unselected package libdeflate0:arm64. 176s Preparing to unpack .../01-libdeflate0_1.19-1_arm64.deb ... 176s Unpacking libdeflate0:arm64 (1.19-1) ... 176s Selecting previously unselected package libgfortran5:arm64. 176s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 176s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 176s Selecting previously unselected package libhtscodecs2:arm64. 176s Preparing to unpack .../03-libhtscodecs2_1.6.0-1_arm64.deb ... 176s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 176s Selecting previously unselected package libhts3:arm64. 176s Preparing to unpack .../04-libhts3_1.18+ds-1_arm64.deb ... 176s Unpacking libhts3:arm64 (1.18+ds-1) ... 176s Selecting previously unselected package liblapack3:arm64. 176s Preparing to unpack .../05-liblapack3_3.12.0-3_arm64.deb ... 176s Unpacking liblapack3:arm64 (3.12.0-3) ... 176s Selecting previously unselected package python3-all. 176s Preparing to unpack .../06-python3-all_3.12.1-0ubuntu2_arm64.deb ... 176s Unpacking python3-all (3.12.1-0ubuntu2) ... 176s Selecting previously unselected package python3-numpy. 176s Preparing to unpack .../07-python3-numpy_1%3a1.24.2-2_arm64.deb ... 176s Unpacking python3-numpy (1:1.24.2-2) ... 176s Selecting previously unselected package python3-pysam. 176s Preparing to unpack .../08-python3-pysam_0.22.0+ds-1_arm64.deb ... 176s Unpacking python3-pysam (0.22.0+ds-1) ... 177s Selecting previously unselected package python3-pybedtools. 177s Preparing to unpack .../09-python3-pybedtools_0.9.1-1_arm64.deb ... 177s Unpacking python3-pybedtools (0.9.1-1) ... 177s Selecting previously unselected package autopkgtest-satdep. 177s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 177s Unpacking autopkgtest-satdep (0) ... 177s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 177s Setting up libdeflate0:arm64 (1.19-1) ... 177s Setting up python3-all (3.12.1-0ubuntu2) ... 177s Setting up libblas3:arm64 (3.12.0-3) ... 177s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 177s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 177s Setting up liblapack3:arm64 (3.12.0-3) ... 177s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 177s Setting up libhts3:arm64 (1.18+ds-1) ... 177s Setting up python3-pysam (0.22.0+ds-1) ... 177s Setting up python3-numpy (1:1.24.2-2) ... 179s Setting up python3-pybedtools (0.9.1-1) ... 179s Setting up autopkgtest-satdep (0) ... 179s Processing triggers for man-db (2.12.0-3) ... 179s Processing triggers for libc-bin (2.39-0ubuntu6) ... 182s (Reading database ... 77035 files and directories currently installed.) 182s Removing autopkgtest-satdep (0) ... 183s autopkgtest [17:26:42]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pybedtools; print(pybedtools)" ; done 183s autopkgtest [17:26:42]: test autodep8-python3: [----------------------- 183s Testing with python3.12: 184s 184s autopkgtest [17:26:43]: test autodep8-python3: -----------------------] 184s autopkgtest [17:26:43]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 184s autodep8-python3 PASS (superficial) 185s autopkgtest [17:26:44]: @@@@@@@@@@@@@@@@@@@@ summary 185s autodep8-python3 PASS (superficial) 199s Creating nova instance adt-noble-arm64-python-pybedtools-20240324-170914-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...