0s autopkgtest [16:49:06]: starting date and time: 2024-03-24 16:49:06+0000 0s autopkgtest [16:49:06]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:49:06]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pbc5a_6g/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 htseq --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-3@bos01-arm64-45.secgroup --name adt-noble-arm64-htseq-20240324-164906-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 154s autopkgtest [16:51:40]: testbed dpkg architecture: arm64 154s autopkgtest [16:51:40]: testbed apt version: 2.7.12 154s autopkgtest [16:51:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 155s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3984 kB] 157s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 157s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 157s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 157s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 157s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 157s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 157s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 157s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 158s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 158s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 158s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 163s Fetched 9847 kB in 4s (2362 kB/s) 163s Reading package lists... 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 169s Calculating upgrade... 169s The following packages will be REMOVED: 169s libssl3 169s The following NEW packages will be installed: 169s libssl3t64 169s The following packages have been kept back: 169s curl 169s The following packages will be upgraded: 169s openssl 169s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 169s Need to get 2777 kB of archives. 169s After this operation, 139 kB of additional disk space will be used. 169s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 170s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 171s Fetched 2777 kB in 1s (2629 kB/s) 171s (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.) 171s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 171s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 171s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 171s wget depends on libssl3 (>= 3.0.0). 171s u-boot-tools depends on libssl3 (>= 3.0.0). 171s tnftp depends on libssl3 (>= 3.0.0). 171s tcpdump depends on libssl3 (>= 3.0.0). 171s systemd-resolved depends on libssl3 (>= 3.0.0). 171s systemd depends on libssl3 (>= 3.0.0). 171s sudo depends on libssl3 (>= 3.0.0). 171s sbsigntool depends on libssl3 (>= 3.0.0). 171s rsync depends on libssl3 (>= 3.0.0). 171s python3-cryptography depends on libssl3 (>= 3.0.0). 171s openssh-server depends on libssl3 (>= 3.0.10). 171s openssh-client depends on libssl3 (>= 3.0.10). 171s mtd-utils depends on libssl3 (>= 3.0.0). 171s mokutil depends on libssl3 (>= 3.0.0). 171s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 171s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 171s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 171s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 171s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 171s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 171s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 171s libnvme1 depends on libssl3 (>= 3.0.0). 171s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 171s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 171s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 171s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 171s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 171s kmod depends on libssl3 (>= 3.0.0). 171s dhcpcd-base depends on libssl3 (>= 3.0.0). 171s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 171s 172s (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.) 172s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 172s Selecting previously unselected package libssl3t64:arm64. 172s (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.) 172s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 172s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 172s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 172s Setting up openssl (3.0.13-0ubuntu2) ... 172s Processing triggers for man-db (2.12.0-3) ... 173s Processing triggers for libc-bin (2.39-0ubuntu6) ... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 175s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 177s sh: Attempting to set up Debian/Ubuntu apt sources automatically 177s Reading package lists...sh: Distribution appears to be Ubuntu 177s 178s Building dependency tree... 178s Reading state information... 179s eatmydata is already the newest version (131-1). 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s dbus is already the newest version (1.14.10-4ubuntu1). 180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 180s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s rng-tools-debian is already the newest version (2.4). 182s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 183s The following packages will be REMOVED: 183s cloud-init* python3-configobj* python3-debconf* 184s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 184s After this operation, 3256 kB disk space will be freed. 184s (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.) 184s Removing cloud-init (24.1.2-0ubuntu1) ... 185s Removing python3-configobj (5.0.8-3) ... 185s Removing python3-debconf (1.5.86) ... 185s Processing triggers for man-db (2.12.0-3) ... 186s (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.) 186s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 187s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 187s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 187s invoke-rc.d: policy-rc.d denied execution of try-restart. 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s linux-generic is already the newest version (6.8.0-11.11+1). 189s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 190s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 190s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 195s Reading package lists... 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 196s Calculating upgrade... 197s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 199s autopkgtest [16:52:25]: rebooting testbed after setup commands that affected boot 352s autopkgtest [16:54:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 355s autopkgtest [16:55:01]: @@@@@@@@@@@@@@@@@@@@ apt-source htseq 360s Get:1 http://ftpmaster.internal/ubuntu noble/universe htseq 2.0.5-1 (dsc) [2164 B] 360s Get:2 http://ftpmaster.internal/ubuntu noble/universe htseq 2.0.5-1 (tar) [36.8 MB] 360s Get:3 http://ftpmaster.internal/ubuntu noble/universe htseq 2.0.5-1 (diff) [11.2 kB] 360s gpgv: Signature made Fri Jan 12 05:59:53 2024 UTC 360s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 360s gpgv: issuer "tille@debian.org" 360s gpgv: Can't check signature: No public key 360s dpkg-source: warning: cannot verify inline signature for ./htseq_2.0.5-1.dsc: no acceptable signature found 362s autopkgtest [16:55:08]: testing package htseq version 2.0.5-1 362s autopkgtest [16:55:08]: build not needed 367s autopkgtest [16:55:13]: test autodep8-python3: preparing testbed 369s Reading package lists... 369s Building dependency tree... 369s Reading state information... 370s Starting pkgProblemResolver with broken count: 0 370s Starting 2 pkgProblemResolver with broken count: 0 370s Done 371s The following additional packages will be installed: 371s libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 liblapack3 371s python3-all python3-htseq python3-numpy python3-pysam 371s Suggested packages: 371s gcc gfortran python3-dev python3-pytest 371s The following NEW packages will be installed: 371s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 371s liblapack3 python3-all python3-htseq python3-numpy python3-pysam 371s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 371s Need to get 12.8 MB/12.8 MB of archives. 371s After this operation, 79.0 MB of additional disk space will be used. 371s Get:1 /tmp/autopkgtest.UcCF7J/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 371s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 372s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 372s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 372s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 372s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 372s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 372s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 372s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 372s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 372s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-htseq arm64 2.0.5-1 [479 kB] 373s Fetched 12.8 MB in 1s (10.2 MB/s) 373s Selecting previously unselected package libblas3:arm64. 373s (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.) 373s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ... 373s Unpacking libblas3:arm64 (3.12.0-3) ... 373s Selecting previously unselected package libdeflate0:arm64. 373s Preparing to unpack .../01-libdeflate0_1.19-1_arm64.deb ... 373s Unpacking libdeflate0:arm64 (1.19-1) ... 373s Selecting previously unselected package libgfortran5:arm64. 373s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 373s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 373s Selecting previously unselected package libhtscodecs2:arm64. 373s Preparing to unpack .../03-libhtscodecs2_1.6.0-1_arm64.deb ... 373s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 373s Selecting previously unselected package libhts3:arm64. 373s Preparing to unpack .../04-libhts3_1.18+ds-1_arm64.deb ... 373s Unpacking libhts3:arm64 (1.18+ds-1) ... 373s Selecting previously unselected package liblapack3:arm64. 373s Preparing to unpack .../05-liblapack3_3.12.0-3_arm64.deb ... 373s Unpacking liblapack3:arm64 (3.12.0-3) ... 374s Selecting previously unselected package python3-all. 374s Preparing to unpack .../06-python3-all_3.12.1-0ubuntu2_arm64.deb ... 374s Unpacking python3-all (3.12.1-0ubuntu2) ... 374s Selecting previously unselected package python3-numpy. 374s Preparing to unpack .../07-python3-numpy_1%3a1.24.2-2_arm64.deb ... 374s Unpacking python3-numpy (1:1.24.2-2) ... 374s Selecting previously unselected package python3-pysam. 374s Preparing to unpack .../08-python3-pysam_0.22.0+ds-1_arm64.deb ... 374s Unpacking python3-pysam (0.22.0+ds-1) ... 375s Selecting previously unselected package python3-htseq. 375s Preparing to unpack .../09-python3-htseq_2.0.5-1_arm64.deb ... 375s Unpacking python3-htseq (2.0.5-1) ... 375s Selecting previously unselected package autopkgtest-satdep. 375s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 375s Unpacking autopkgtest-satdep (0) ... 375s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 375s Setting up libdeflate0:arm64 (1.19-1) ... 375s Setting up python3-all (3.12.1-0ubuntu2) ... 375s Setting up libblas3:arm64 (3.12.0-3) ... 375s 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 375s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 375s Setting up liblapack3:arm64 (3.12.0-3) ... 375s 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 375s Setting up libhts3:arm64 (1.18+ds-1) ... 375s Setting up python3-pysam (0.22.0+ds-1) ... 375s Setting up python3-numpy (1:1.24.2-2) ... 379s Setting up python3-htseq (2.0.5-1) ... 379s /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\=' 379s _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$") 379s /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s' 379s _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)") 379s /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s' 379s _re_attr_empty = re.compile("^\s*$") 379s /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s' 379s _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)") 379s Setting up autopkgtest-satdep (0) ... 379s Processing triggers for man-db (2.12.0-3) ... 380s Processing triggers for libc-bin (2.39-0ubuntu6) ... 385s (Reading database ... 76930 files and directories currently installed.) 385s Removing autopkgtest-satdep (0) ... 385s autopkgtest [16:55:31]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import HTSeq; print(HTSeq)" ; done 385s autopkgtest [16:55:31]: test autodep8-python3: [----------------------- 386s Testing with python3.12: 386s 386s autopkgtest [16:55:32]: test autodep8-python3: -----------------------] 387s autopkgtest [16:55:33]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 387s autodep8-python3 PASS (superficial) 387s autopkgtest [16:55:33]: @@@@@@@@@@@@@@@@@@@@ summary 387s autodep8-python3 PASS (superficial) 400s Creating nova instance adt-noble-arm64-htseq-20240324-164906-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...