0s autopkgtest [01:53:31]: starting date and time: 2024-03-20 01:53:31+0000
  0s autopkgtest [01:53:31]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [01:53:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5zn4asv1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:jellyfish,src:booth,src:cmake,src:cod-tools,src:curl,src:cyrus-imapd,src:db5.3,src:feature-check,src:gdbm,src:gearmand,src:gnutls28,src:gromacs,src:htslib,src:inn2,src:konclude,src:libdbd-mariadb-perl,src:libdbd-mysql-perl,src:libpsl,src:libwebsockets,src:lighttpd,src:mmdebstrap,src:netatalk,src:nettle,src:openbsd-inetd,src:openssl,src:perl,src:postgresql-16,src:puppet-lint,src:puppet-module-puppetlabs-stdlib,src:spiped,src:systemd,src:zile --apt-upgrade crac --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=jellyfish/2.3.1-3 booth/1.1-1ubuntu3 cmake/3.28.3-1build5 cod-tools/3.8.1+dfsg-1build2 curl/8.5.0-2ubuntu7 cyrus-imapd/3.8.1-3build2 db5.3/5.3.28+dfsg2-5build1 feature-check/2.1.0-2 gdbm/1.23-5.1 gearmand/1.1.20+ds-1.2 gnutls28/3.8.3-1.1ubuntu2 gromacs/2023.3-1ubuntu2 htslib/1.19+ds-1.1build2 inn2/2.7.2~20240212-1build2 konclude/0.7.0+1138+git20220514~dfsg-1build1 libdbd-mariadb-perl/1.22-1build3 libdbd-mysql-perl/4.052-1ubuntu2 libpsl/0.21.2-1.1 libwebsockets/4.3.3-1.1build1 lighttpd/1.4.74-1ubuntu2 mmdebstrap/1.4.3-6 netatalk/3.1.18~ds-1build2 nettle/3.9.1-2.2 openbsd-inetd/0.20221205-3build2 openssl/3.0.13-0ubuntu2 perl/5.38.2-3.2 postgresql-16/16.2-1ubuntu2 puppet-lint/4.2.4-2 puppet-module-puppetlabs-stdlib/9.4.1-1 spiped/1.6.2-3build1 systemd/255.4-1ubuntu5 zile/2.6.2-2build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-8.secgroup --name adt-noble-arm64-crac-20240320-015331-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/
144s autopkgtest [01:55:55]: testbed dpkg architecture: arm64
145s autopkgtest [01:55:56]: testbed apt version: 2.7.12
145s autopkgtest [01:55:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup
146s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
146s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB]
146s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
146s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB]
146s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3803 kB]
147s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [665 kB]
147s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
147s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [41.7 kB]
147s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
147s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4163 kB]
147s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
147s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [56.7 kB]
147s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
152s Fetched 9409 kB in 3s (3727 kB/s)
152s Reading package lists...
156s Reading package lists...
157s Building dependency tree...
157s Reading state information...
157s Calculating upgrade...
158s The following packages were automatically installed and are no longer required:
158s   libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38
158s Use 'sudo apt autoremove' to remove them.
158s The following packages will be REMOVED:
158s   dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 libssl3 perl
158s The following NEW packages will be installed:
158s   libgdbm-compat4t64 libgdbm6t64 libssl3t64
158s The following packages have been kept back:
158s   curl
158s The following packages will be upgraded:
158s   libnss-systemd libpam-systemd libsystemd-shared libsystemd0 libudev1 openssl
158s   perl-base perl-modules-5.38 systemd systemd-dev systemd-resolved
158s   systemd-sysv systemd-timesyncd ubuntu-minimal ubuntu-standard udev
158s 16 upgraded, 3 newly installed, 6 to remove and 1 not upgraded.
158s Need to get 16.4 MB of archives.
158s After this operation, 4059 kB disk space will be freed.
158s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB]
159s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB]
159s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B]
159s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-resolved arm64 255.4-1ubuntu5 [291 kB]
159s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnss-systemd arm64 255.4-1ubuntu5 [154 kB]
159s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.4-1ubuntu5 [103 kB]
159s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB]
159s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.4-1ubuntu5 [3403 kB]
160s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 udev arm64 255.4-1ubuntu5 [1852 kB]
160s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.4-1ubuntu5 [11.9 kB]
160s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-systemd arm64 255.4-1ubuntu5 [232 kB]
160s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB]
160s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-timesyncd arm64 255.4-1ubuntu5 [34.8 kB]
160s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.4-1ubuntu5 [2016 kB]
160s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.4-1ubuntu5 [173 kB]
160s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.4-1ubuntu5 [424 kB]
160s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
160s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536build1 [10.7 kB]
160s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536build1 [10.7 kB]
161s Fetched 16.4 MB in 2s (7320 kB/s)
161s (Reading database ... 
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(Reading database ... 75850 files and directories currently installed.)
161s Removing dpkg-dev (1.22.4ubuntu5) ...
161s Removing libdpkg-perl (1.22.4ubuntu5) ...
161s Removing perl (5.38.2-3) ...
161s (Reading database ... 
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(Reading database ... 75269 files and directories currently installed.)
161s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ...
161s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
162s Setting up perl-base (5.38.2-3.2) ...
162s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested:
162s  python3-gdbm:arm64 depends on libgdbm6 (>= 1.16).
162s  man-db depends on libgdbm6 (>= 1.16).
162s  libperl5.38:arm64 depends on libgdbm6 (>= 1.21).
162s  libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16).
162s 
162s (Reading database ... 
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(Reading database ... 75269 files and directories currently installed.)
162s Removing libgdbm6:arm64 (1.23-5) ...
162s Selecting previously unselected package libgdbm6t64:arm64.
162s (Reading database ... 
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(Reading database ... 75264 files and directories currently installed.)
162s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ...
162s Unpacking libgdbm6t64:arm64 (1.23-5.1) ...
162s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested:
162s  libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3).
162s 
162s (Reading database ... 
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(Reading database ... 75270 files and directories currently installed.)
162s Removing libgdbm-compat4:arm64 (1.23-5) ...
162s Selecting previously unselected package libgdbm-compat4t64:arm64.
162s (Reading database ... 
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162s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ...
162s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
162s Preparing to unpack .../systemd-resolved_255.4-1ubuntu5_arm64.deb ...
162s Unpacking systemd-resolved (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
162s Preparing to unpack .../libnss-systemd_255.4-1ubuntu5_arm64.deb ...
162s Unpacking libnss-systemd:arm64 (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
163s Preparing to unpack .../systemd-dev_255.4-1ubuntu5_all.deb ...
163s Unpacking systemd-dev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
163s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
163s  wget depends on libssl3 (>= 3.0.0).
163s  u-boot-tools depends on libssl3 (>= 3.0.0).
163s  tnftp depends on libssl3 (>= 3.0.0).
163s  tcpdump depends on libssl3 (>= 3.0.0).
163s  systemd depends on libssl3 (>= 3.0.0).
163s  sudo depends on libssl3 (>= 3.0.0).
163s  sbsigntool depends on libssl3 (>= 3.0.0).
163s  rsync depends on libssl3 (>= 3.0.0).
163s  python3-cryptography depends on libssl3 (>= 3.0.0).
163s  openssl depends on libssl3 (>= 3.0.9).
163s  openssh-server depends on libssl3 (>= 3.0.10).
163s  openssh-client depends on libssl3 (>= 3.0.10).
163s  mtd-utils depends on libssl3 (>= 3.0.0).
163s  mokutil depends on libssl3 (>= 3.0.0).
163s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
163s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
163s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
163s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
163s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
163s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
163s  libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0).
163s  libnvme1 depends on libssl3 (>= 3.0.0).
163s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
163s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
163s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
163s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
163s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
163s  kmod depends on libssl3 (>= 3.0.0).
163s  dhcpcd-base depends on libssl3 (>= 3.0.0).
163s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
163s 
163s (Reading database ... 
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(Reading database ... 75271 files and directories currently installed.)
163s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
163s Selecting previously unselected package libssl3t64:arm64.
163s (Reading database ... 
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(Reading database ... 75260 files and directories currently installed.)
163s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ...
163s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ...
163s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ...
163s (Reading database ... 
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(Reading database ... 75273 files and directories currently installed.)
163s Preparing to unpack .../systemd_255.4-1ubuntu5_arm64.deb ...
163s Unpacking systemd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
164s Preparing to unpack .../udev_255.4-1ubuntu5_arm64.deb ...
164s Unpacking udev (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
164s Preparing to unpack .../libsystemd-shared_255.4-1ubuntu5_arm64.deb ...
164s Unpacking libsystemd-shared:arm64 (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
164s Setting up libsystemd-shared:arm64 (255.4-1ubuntu5) ...
164s (Reading database ... 
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(Reading database ... 75273 files and directories currently installed.)
164s Preparing to unpack .../libsystemd0_255.4-1ubuntu5_arm64.deb ...
164s Unpacking libsystemd0:arm64 (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
164s Setting up libsystemd0:arm64 (255.4-1ubuntu5) ...
164s Setting up systemd-dev (255.4-1ubuntu5) ...
164s Setting up systemd (255.4-1ubuntu5) ...
166s (Reading database ... 
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166s Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_arm64.deb ...
166s Unpacking systemd-sysv (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
166s Preparing to unpack .../libpam-systemd_255.4-1ubuntu5_arm64.deb ...
166s Unpacking libpam-systemd:arm64 (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
166s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ...
166s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
166s Preparing to unpack .../systemd-timesyncd_255.4-1ubuntu5_arm64.deb ...
166s Unpacking systemd-timesyncd (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
166s Preparing to unpack .../libudev1_255.4-1ubuntu5_arm64.deb ...
166s Unpacking libudev1:arm64 (255.4-1ubuntu5) over (255.2-3ubuntu2) ...
166s Setting up libudev1:arm64 (255.4-1ubuntu5) ...
166s (Reading database ... 
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(Reading database ... 75273 files and directories currently installed.)
166s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
166s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
167s Preparing to unpack .../ubuntu-minimal_1.536build1_arm64.deb ...
167s Unpacking ubuntu-minimal (1.536build1) over (1.536) ...
167s Preparing to unpack .../ubuntu-standard_1.536build1_arm64.deb ...
167s Unpacking ubuntu-standard (1.536build1) over (1.536) ...
167s Setting up systemd-sysv (255.4-1ubuntu5) ...
167s Setting up libgdbm6t64:arm64 (1.23-5.1) ...
167s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
167s Setting up libnss-systemd:arm64 (255.4-1ubuntu5) ...
167s Setting up perl-modules-5.38 (5.38.2-3.2) ...
167s Setting up systemd-timesyncd (255.4-1ubuntu5) ...
168s Setting up udev (255.4-1ubuntu5) ...
170s Setting up libpam-systemd:arm64 (255.4-1ubuntu5) ...
170s Setting up openssl (3.0.13-0ubuntu2) ...
170s Setting up systemd-resolved (255.4-1ubuntu5) ...
171s Setting up ubuntu-minimal (1.536build1) ...
171s Setting up ubuntu-standard (1.536build1) ...
171s Processing triggers for dbus (1.14.10-4ubuntu1) ...
171s Processing triggers for initramfs-tools (0.142ubuntu20) ...
171s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
171s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
190s System running in EFI mode, skipping.
190s Processing triggers for libc-bin (2.39-0ubuntu2) ...
190s Processing triggers for man-db (2.12.0-3) ...
192s Reading package lists...
192s Building dependency tree...
192s Reading state information...
193s The following packages will be REMOVED:
193s   libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38*
194s 0 upgraded, 0 newly installed, 5 to remove and 1 not upgraded.
194s After this operation, 52.0 MB disk space will be freed.
194s (Reading database ... 
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194s Removing libperl5.38:arm64 (5.38.2-3) ...
194s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ...
194s Removing lto-disabled-list (47) ...
194s Removing make (4.3-4.1build1) ...
194s Removing perl-modules-5.38 (5.38.2-3.2) ...
194s Processing triggers for man-db (2.12.0-3) ...
194s Processing triggers for libc-bin (2.39-0ubuntu2) ...
195s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
195s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
195s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
195s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
198s Reading package lists...
198s Reading package lists...
199s Building dependency tree...
199s Reading state information...
199s Calculating upgrade...
200s The following packages have been kept back:
200s   curl
200s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
200s Reading package lists...
200s Building dependency tree...
200s Reading state information...
201s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
202s autopkgtest [01:56:53]: rebooting testbed after setup commands that affected boot
358s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
366s autopkgtest [01:59:37]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
368s autopkgtest [01:59:39]: @@@@@@@@@@@@@@@@@@@@ apt-source crac
375s Reading package lists...
375s Building dependency tree...
375s Reading state information...
376s Starting pkgProblemResolver with broken count: 0
376s Starting 2 pkgProblemResolver with broken count: 0
376s Done
377s The following additional packages will be installed:
377s   dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64
377s   lto-disabled-list make perl perl-modules-5.38
377s Suggested packages:
377s   debian-keyring gcc | c-compiler git bzr make-doc perl-doc
377s   libterm-readline-gnu-perl | libterm-readline-perl-perl
377s   libtap-harness-archive-perl
377s Recommended packages:
377s   build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl
377s   libfile-fcntllock-perl
377s The following packages will be REMOVED:
377s   libdb5.3
377s The following NEW packages will be installed:
377s   autopkgtest-satdep dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64
377s   libperl5.38t64 lto-disabled-list make perl perl-modules-5.38
377s 0 upgraded, 10 newly installed, 1 to remove and 1 not upgraded.
377s Need to get 7257 kB/10.4 MB of archives.
377s After this operation, 56.1 MB of additional disk space will be used.
377s Get:1 /tmp/autopkgtest.DVKRnR/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B]
377s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5build1 [719 kB]
377s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB]
378s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB]
378s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB]
378s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB]
378s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB]
378s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB]
379s Fetched 7257 kB in 1s (5775 kB/s)
379s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested:
379s  libsasl2-modules-db:arm64 depends on libdb5.3.
379s  libpython3.12-stdlib:arm64 depends on libdb5.3.
379s  libpython3.11-stdlib:arm64 depends on libdb5.3.
379s  libpam-modules:arm64 depends on libdb5.3.
379s  iproute2 depends on libdb5.3.
379s  apt-utils depends on libdb5.3.
379s 
379s (Reading database ... 
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(Reading database ... 73302 files and directories currently installed.)
379s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ...
379s Selecting previously unselected package libdb5.3t64:arm64.
379s (Reading database ... 
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(Reading database ... 73296 files and directories currently installed.)
379s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5build1_arm64.deb ...
379s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5build1) ...
379s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5build1) ...
379s Selecting previously unselected package perl-modules-5.38.
379s (Reading database ... 
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(Reading database ... 73302 files and directories currently installed.)
379s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ...
379s Unpacking perl-modules-5.38 (5.38.2-3.2) ...
380s Selecting previously unselected package libgdbm-compat4t64:arm64.
380s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ...
380s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
380s Selecting previously unselected package libperl5.38t64:arm64.
380s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ...
380s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ...
380s Selecting previously unselected package perl.
380s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ...
380s Unpacking perl (5.38.2-3.2) ...
380s Selecting previously unselected package libdpkg-perl.
380s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ...
380s Unpacking libdpkg-perl (1.22.4ubuntu5) ...
380s Selecting previously unselected package make.
380s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ...
380s Unpacking make (4.3-4.1build1) ...
380s Selecting previously unselected package lto-disabled-list.
380s Preparing to unpack .../6-lto-disabled-list_47_all.deb ...
380s Unpacking lto-disabled-list (47) ...
380s Selecting previously unselected package dpkg-dev.
380s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ...
380s Unpacking dpkg-dev (1.22.4ubuntu5) ...
381s Selecting previously unselected package autopkgtest-satdep.
381s Preparing to unpack .../8-1-autopkgtest-satdep.deb ...
381s Unpacking autopkgtest-satdep (0) ...
381s Setting up lto-disabled-list (47) ...
381s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
381s Setting up make (4.3-4.1build1) ...
381s Setting up perl-modules-5.38 (5.38.2-3.2) ...
381s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ...
381s Setting up perl (5.38.2-3.2) ...
381s Setting up libdpkg-perl (1.22.4ubuntu5) ...
381s Setting up dpkg-dev (1.22.4ubuntu5) ...
381s Setting up autopkgtest-satdep (0) ...
381s Processing triggers for man-db (2.12.0-3) ...
382s Processing triggers for libc-bin (2.39-0ubuntu2) ...
385s (Reading database ... 75854 files and directories currently installed.)
385s Removing autopkgtest-satdep (0) ...
386s Get:1 http://ftpmaster.internal/ubuntu noble/universe crac 2.5.2+dfsg-5 (dsc) [2081 B]
386s Get:2 http://ftpmaster.internal/ubuntu noble/universe crac 2.5.2+dfsg-5 (tar) [658 kB]
386s Get:3 http://ftpmaster.internal/ubuntu noble/universe crac 2.5.2+dfsg-5 (diff) [15.1 kB]
387s gpgv: Signature made Sun Nov  7 21:33:37 2021 UTC
387s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
387s gpgv:                issuer "tille@debian.org"
387s gpgv: Can't check signature: No public key
387s dpkg-source: warning: cannot verify inline signature for ./crac_2.5.2+dfsg-5.dsc: no acceptable signature found
387s autopkgtest [01:59:58]: testing package crac version 2.5.2+dfsg-5
387s autopkgtest [01:59:58]: build not needed
388s autopkgtest [01:59:59]: test run-unit-test: preparing testbed
397s Reading package lists...
398s Building dependency tree...
398s Reading state information...
398s Starting pkgProblemResolver with broken count: 0
399s Starting 2 pkgProblemResolver with broken count: 0
399s Done
400s The following additional packages will be installed:
400s   crac libdeflate0 libgkarrays1 libgzstream0 libhts3 libhtscodecs2
400s   libjellyfish-2.0-2
400s The following NEW packages will be installed:
400s   autopkgtest-satdep crac libdeflate0 libgkarrays1 libgzstream0 libhts3
400s   libhtscodecs2 libjellyfish-2.0-2
400s 0 upgraded, 8 newly installed, 0 to remove and 1 not upgraded.
400s Need to get 1140 kB/1140 kB of archives.
400s After this operation, 4003 kB of additional disk space will be used.
400s Get:1 /tmp/autopkgtest.DVKRnR/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B]
400s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libgkarrays1 arm64 2.1.0+dfsg-4 [46.7 kB]
400s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libgzstream0 arm64 1.5+git20171107.9a20658-1 [7406 B]
400s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
400s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
400s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
400s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libjellyfish-2.0-2 arm64 2.3.1-3 [66.1 kB]
400s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 crac arm64 2.5.2+dfsg-5 [476 kB]
401s Fetched 1140 kB in 1s (1739 kB/s)
401s Selecting previously unselected package libgkarrays1.
401s (Reading database ... 
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(Reading database ... 75854 files and directories currently installed.)
401s Preparing to unpack .../0-libgkarrays1_2.1.0+dfsg-4_arm64.deb ...
401s Unpacking libgkarrays1 (2.1.0+dfsg-4) ...
401s Selecting previously unselected package libgzstream0:arm64.
401s Preparing to unpack .../1-libgzstream0_1.5+git20171107.9a20658-1_arm64.deb ...
401s Unpacking libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
401s Selecting previously unselected package libdeflate0:arm64.
401s Preparing to unpack .../2-libdeflate0_1.19-1_arm64.deb ...
401s Unpacking libdeflate0:arm64 (1.19-1) ...
401s Selecting previously unselected package libhtscodecs2:arm64.
401s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_arm64.deb ...
401s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
401s Selecting previously unselected package libhts3:arm64.
401s Preparing to unpack .../4-libhts3_1.18+ds-1_arm64.deb ...
401s Unpacking libhts3:arm64 (1.18+ds-1) ...
401s Selecting previously unselected package libjellyfish-2.0-2:arm64.
401s Preparing to unpack .../5-libjellyfish-2.0-2_2.3.1-3_arm64.deb ...
401s Unpacking libjellyfish-2.0-2:arm64 (2.3.1-3) ...
401s Selecting previously unselected package crac.
401s Preparing to unpack .../6-crac_2.5.2+dfsg-5_arm64.deb ...
401s Unpacking crac (2.5.2+dfsg-5) ...
401s Selecting previously unselected package autopkgtest-satdep.
401s Preparing to unpack .../7-2-autopkgtest-satdep.deb ...
401s Unpacking autopkgtest-satdep (0) ...
401s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
401s Setting up libgkarrays1 (2.1.0+dfsg-4) ...
401s Setting up libdeflate0:arm64 (1.19-1) ...
401s Setting up libjellyfish-2.0-2:arm64 (2.3.1-3) ...
401s Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-1) ...
401s Setting up libhts3:arm64 (1.18+ds-1) ...
401s Setting up crac (2.5.2+dfsg-5) ...
401s Setting up autopkgtest-satdep (0) ...
401s Processing triggers for man-db (2.12.0-3) ...
402s Processing triggers for libc-bin (2.39-0ubuntu2) ...
406s (Reading database ... 76024 files and directories currently installed.)
406s Removing autopkgtest-satdep (0) ...
407s autopkgtest [02:00:18]: test run-unit-test: [-----------------------
409s Launching ' crac -i ../../test_f/cigar/genome -r reads.fasta -k 22 -o ../../test_f/cigar/consistency.sam --detailed-sam --reads-index GKARRAYS --use-x-in-cigar --min-chimera-score 0'
409s ==> ../../test_f/cigar/consistency.tap
410s 
410s Launching ' crac -i ../../test_f/cigar/genome -r reads_sam1.fasta reads_sam2.fasta -k 10 -o ../../test_f/cigar/consistency3.sam --treat-multiple 100 --use-x-in-cigar'
410s ==> ../../test_f/cigar/consistency3.tap
410s 
410s Launching ' crac -i ../../test_f/cigar/genome -r reads_k18.fasta -k 18 -o ../../test_f/cigar/consistency2.sam'
410s ==> ../../test_f/cigar/consistency2.tap
410s 
410s Launching ' crac -i ../../test_f/causes/genome -r snp.fa -k 22 --deep-snv --nb-nucleotides-snv-comparison 3 -o ../../test_f/causes/snp.sam --detailed-sam --use-x-in-cigar'
410s ==> ../../test_f/causes/snp.fa.tap
410s 
410s Launching ' crac -i ../../test_f/causes/genome -r biotag.fa -k 22 -o ../../test_f/causes/biotag.sam --detailed-sam --use-x-in-cigar'
410s ==> ../../test_f/causes/biotag.fa.tap
410s 
410s Launching ' crac -i ../../test_f/splices_adjust/genome -r splice.fa -k 22 -o ../../test_f/splices_adjust/splice.sam --detailed-sam'
410s ==> ../../test_f/splices_adjust/splice.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15605_2-genome -r bug-15605_2-read.fa -k 22 -o ../../test_f/bug/bug-15605_2.sam --detailed-sam'
411s ==> ../../test_f/bug/bug-15605_2.tap
411s 
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15639-genome -r bug-15639-read.fa -k 22 -o ../../test_f/bug/bug-15639.sam'
411s ==> ../../test_f/bug/bug-15639.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-16581-genome -r bug-16581-read.fq -m 25 -k 22 -o ../../test_f/bug/bug-16581.sam'
411s ==> ../../test_f/bug/bug-16581.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15605-genome -r bug-15605-read.fa -k 22 -o ../../test_f/bug/bug-15605.sam --detailed-sam'
411s ==> ../../test_f/bug/bug-15605.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-17175-genome -r bug-17175-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-17175.sam --use-x-in-cigar'
411s ==> ../../test_f/bug/bug-17175.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15672-genome -r bug-15672-read.fa -k 22 -o ../../test_f/bug/bug-15672.sam --detailed-sam'
411s ==> ../../test_f/bug/bug-15672.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-case-sensitive-genome -r bug-case-sensitive-read.fa -k 12 -o ../../test_f/bug/bug-case-sensitive.sam --detailed-sam'
411s ==> ../../test_f/bug/bug-case-sensitive.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-18793-genome -r bug-18793-read.fa -k 22 -o ../../test_f/bug/bug-18793.sam --detailed-sam --reads-index GKARRAYS'
411s ==> ../../test_f/bug/bug-18793.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-18522-genome -r bug-18522-read.fa -k 10 -o ../../test_f/bug/bug-18522.sam --treat-multiple 2'
411s ==> ../../test_f/bug/bug-18522.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15649-genome-2 -r bug-15649-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15649-2.sam'
411s ==> ../../test_f/bug/bug-15649-2.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-18524-genome -r bug-18524-read.fa -k 22 -o ../../test_f/bug/bug-18524.sam --detailed-sam'
411s ==> ../../test_f/bug/bug-18524.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-18409-genome -r bug-18409-read.fa --detailed-sam -k 22 -o /dev/stdout | tr ';' '\n''
411s ==> ./bug-18409.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15677-genome -r bug-15677-read.fa -k 22 -o ../../test_f/bug/bug-15677.sam'
411s ==> ../../test_f/bug/bug-15677.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-16403-genome -r bug-16403-read.fa -k 20 -o ../../test_f/bug/bug-16931.sam'
411s ==> ../../test_f/bug/bug-16931.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-18568-genome -r bug-18568-read.fa -k 22 -o ../../test_f/bug/bug-18568.sam --detailed-sam --reads-index GKARRAYS'
411s ==> ../../test_f/bug/bug-18568.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15646-genome -r bug-15646-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15646.sam'
411s ==> ../../test_f/bug/bug-15646.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-18180-genome -r bug-18180-read.fa --detailed-sam --emt -k 18 -o ../../test_f/bug/bug-18180.sam'
411s Warning: Running CRAC--emt with k=18 which means that it only maps the first located kmer of length 18 for each read
411s ==> ../../test_f/bug/bug-18180.tap
411s 
411s Launching ' crac -i ../../test_f/bug/bug-15630-genome -r bug-15630-read.fa --detailed-sam -k 18 -o ../../test_f/bug/bug-15630.sam'
411s ==> ../../test_f/bug/bug-15630.tap
412s 
412s Launching ' crac -i ../../test_f/bug/bug-15847-genome -r bug-15847-read.fa -k 22 --treat-multiple 36 --detailed-sam -o ../../test_f/bug/bug-15847.sam'
412s ==> ../../test_f/bug/bug-15847.tap
412s 
412s Launching ' crac -i ../../test_f/bug/bug-17749-genome -r bug-17749-read.fa -k 22 -o ../../test_f/bug/bug-17749.sam --max-splice-length 100 --max-extension-length 2 --min-chimera-score 0'
412s ==> ../../test_f/bug/bug-17749.tap
412s 
412s Launching ' crac -i ../../test_f/bug/bug-15649-genome -r bug-15649-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15649.sam'
412s ==> ../../test_f/bug/bug-15649.tap
412s 
412s Launching ' crac -i ../../test_f/bug/bug-2015-12-08-genome -r bug-2015-12-08-read1.fa bug-2015-12-08-read2.fa -k 22 -o ../../test_f/bug/bug-2015-12-08.sam --detailed-sam --reads-index GKARRAYS'
412s ==> ../../test_f/bug/bug-2015-12-08.tap
412s 
412s Launching ' crac -i ../../test_f/bug/bug-16502-genome -r bug-16502-read.fa -k 22 -o ../../test_f/bug/bug-16502.sam --reads-index GKARRAYS'
412s ==> ../../test_f/bug/bug-16502.tap
412s 
412s Launching ' crac -i ../../test_f/bug/bug-18435-genome -r bug-18435-read.fa -k 22 -o ../../test_f/bug/bug-18435.sam'
412s ==> ../../test_f/bug/bug-18435.tap
412s 
413s autopkgtest [02:00:24]: test run-unit-test: -----------------------]
414s run-unit-test        PASS
414s autopkgtest [02:00:25]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
414s autopkgtest [02:00:25]: @@@@@@@@@@@@@@@@@@@@ summary
414s run-unit-test        PASS
434s Creating nova instance adt-noble-arm64-crac-20240320-015331-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240319.img (UUID bd25b89b-8264-4402-95d9-d9c88f21f275)...