3s autopkgtest [16:49:29]: starting date and time: 2024-07-12 16:49:29+0000
  3s autopkgtest [16:49:29]: git checkout: fd3bed09 nova: allow more retries for quota issues
  3s autopkgtest [16:49:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qltlmohk/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade gmap --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-8.secgroup --name adt-oracular-arm64-gmap-20240712-164925-juju-7f2275-prod-proposed-migration-environment-3-b74d5e35-dcfa-443f-bc9a-e109ef594fd7 --image adt/ubuntu-oracular-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,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/
129s autopkgtest [16:51:35]: testbed dpkg architecture: arm64
129s autopkgtest [16:51:35]: testbed apt version: 2.9.6
129s autopkgtest [16:51:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup
130s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB]
130s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [343 kB]
130s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B]
130s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB]
130s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B]
130s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [89.7 kB]
130s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 c-n-f Metadata [2104 B]
130s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [43.9 kB]
130s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 c-n-f Metadata [364 B]
130s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [355 kB]
130s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 c-n-f Metadata [7988 B]
130s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [7596 B]
130s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 c-n-f Metadata [276 B]
133s Fetched 1034 kB in 1s (1237 kB/s)
133s Reading package lists...
169s Reading package lists...
169s Building dependency tree...
169s Reading state information...
170s Calculating upgrade...
170s The following packages will be upgraded:
170s   inetutils-telnet libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales
170s   openssh-client openssh-server openssh-sftp-server telnet
171s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
171s Need to get 10.7 MB of archives.
171s After this operation, 28.7 kB disk space will be freed.
171s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-devtools arm64 2.39-3.1ubuntu3 [27.7 kB]
171s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6-dev arm64 2.39-3.1ubuntu3 [1591 kB]
171s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-dev-bin arm64 2.39-3.1ubuntu3 [19.7 kB]
171s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6 arm64 2.39-3.1ubuntu3 [2770 kB]
171s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-bin arm64 2.39-3.1ubuntu3 [579 kB]
171s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-sftp-server arm64 1:9.6p1-3ubuntu17 [36.7 kB]
171s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-server arm64 1:9.6p1-3ubuntu17 [502 kB]
171s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 openssh-client arm64 1:9.6p1-3ubuntu17 [888 kB]
171s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 locales all 2.39-3.1ubuntu3 [4220 kB]
171s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 inetutils-telnet arm64 2:2.5-5ubuntu1 [103 kB]
171s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 telnet all 0.17+2.5-5ubuntu1 [3688 B]
172s Preconfiguring packages ...
172s Fetched 10.7 MB in 1s (10.4 MB/s)
172s (Reading database ... 
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(Reading database ... 78392 files and directories currently installed.)
172s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_arm64.deb ...
172s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
173s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_arm64.deb ...
173s Unpacking libc6-dev:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
173s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_arm64.deb ...
173s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
173s Preparing to unpack .../libc6_2.39-3.1ubuntu3_arm64.deb ...
173s Unpacking libc6:arm64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
173s Setting up libc6:arm64 (2.39-3.1ubuntu3) ...
174s Error: Could not restart systemd, systemd binary not working
174s (Reading database ... 
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174s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_arm64.deb ...
174s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
174s Setting up libc-bin (2.39-3.1ubuntu3) ...
175s (Reading database ... 
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(Reading database ... 78392 files and directories currently installed.)
175s Preparing to unpack .../0-openssh-sftp-server_1%3a9.6p1-3ubuntu17_arm64.deb ...
175s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ...
175s Preparing to unpack .../1-openssh-server_1%3a9.6p1-3ubuntu17_arm64.deb ...
176s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ...
176s Preparing to unpack .../2-openssh-client_1%3a9.6p1-3ubuntu17_arm64.deb ...
176s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ...
177s Preparing to unpack .../3-locales_2.39-3.1ubuntu3_all.deb ...
177s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ...
178s Preparing to unpack .../4-inetutils-telnet_2%3a2.5-5ubuntu1_arm64.deb ...
178s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ...
178s Preparing to unpack .../5-telnet_0.17+2.5-5ubuntu1_all.deb ...
178s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ...
178s Setting up openssh-client (1:9.6p1-3ubuntu17) ...
178s Setting up inetutils-telnet (2:2.5-5ubuntu1) ...
178s Setting up locales (2.39-3.1ubuntu3) ...
180s Generating locales (this might take a while)...
184s   en_US.UTF-8... done
184s Generation complete.
184s Setting up libc-dev-bin (2.39-3.1ubuntu3) ...
184s Setting up libc-devtools (2.39-3.1ubuntu3) ...
184s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ...
184s Setting up telnet (0.17+2.5-5ubuntu1) ...
184s Setting up openssh-server (1:9.6p1-3ubuntu17) ...
184s Installing new version of config file /etc/pam.d/sshd ...
188s Setting up libc6-dev:arm64 (2.39-3.1ubuntu3) ...
188s Processing triggers for systemd (256-1ubuntu1) ...
190s Processing triggers for man-db (2.12.1-2) ...
191s Processing triggers for ufw (0.36.2-6) ...
192s Reading package lists...
193s Building dependency tree...
193s Reading state information...
193s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
194s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease
194s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease
194s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease
194s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
198s Reading package lists...
198s Reading package lists...
198s Building dependency tree...
198s Reading state information...
199s Calculating upgrade...
199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
199s Reading package lists...
199s Building dependency tree...
199s Reading state information...
200s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
212s autopkgtest [16:52:58]: rebooting testbed after setup commands that affected boot
218s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
253s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
345s autopkgtest [16:55:11]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024
375s autopkgtest [16:55:41]: @@@@@@@@@@@@@@@@@@@@ apt-source gmap
379s Get:1 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (dsc) [2191 B]
379s Get:2 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (tar) [2495 kB]
379s Get:3 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (diff) [13.3 kB]
379s gpgv: Signature made Sun May 26 10:21:41 2024 UTC
379s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
379s gpgv:                issuer "emollier@debian.org"
379s gpgv: Can't check signature: No public key
379s dpkg-source: warning: cannot verify inline signature for ./gmap_2024-05-20+ds-1.dsc: no acceptable signature found
380s autopkgtest [16:55:46]: testing package gmap version 2024-05-20+ds-1
380s autopkgtest [16:55:46]: build not needed
390s autopkgtest [16:55:56]: test gmap-tests: preparing testbed
392s Reading package lists...
392s Building dependency tree...
392s Reading state information...
393s Starting pkgProblemResolver with broken count: 0
393s Starting 2 pkgProblemResolver with broken count: 0
393s Done
393s The following additional packages will be installed:
393s   gmap
393s The following NEW packages will be installed:
393s   autopkgtest-satdep gmap
394s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
394s Need to get 5728 kB/5729 kB of archives.
394s After this operation, 44.3 MB of additional disk space will be used.
394s Get:1 /tmp/autopkgtest.u4zgmp/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B]
394s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 gmap arm64 2024-05-20+ds-1 [5728 kB]
395s Fetched 5728 kB in 1s (7463 kB/s)
396s Selecting previously unselected package gmap.
396s (Reading database ... 
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396s Preparing to unpack .../gmap_2024-05-20+ds-1_arm64.deb ...
396s Unpacking gmap (2024-05-20+ds-1) ...
396s Selecting previously unselected package autopkgtest-satdep.
396s Preparing to unpack .../1-autopkgtest-satdep.deb ...
396s Unpacking autopkgtest-satdep (0) ...
397s Setting up gmap (2024-05-20+ds-1) ...
397s Setting up autopkgtest-satdep (0) ...
397s Processing triggers for man-db (2.12.1-2) ...
408s (Reading database ... 78455 files and directories currently installed.)
408s Removing autopkgtest-satdep (0) ...
418s autopkgtest [16:56:24]: test gmap-tests: [-----------------------
419s align.test
419s GMAP version 2024-05-20 called with args: gmap.nosimd -A -g /tmp/tmp.Zlurl7zS3F/tests/ss.chr17test /tmp/tmp.Zlurl7zS3F/tests/ss.her2
419s Finished checking compiler assumptions
419s Starting alignment
419s Processed 1 queries in 0.07 seconds (13.67 queries/sec)
419s coords1.test
419s Opening file /tmp/tmp.Zlurl7zS3F/tests/ss.chr17test
419s   Processed short contigs (<1000000 nt): .
419s ============================================================
419s Contig mapping information has been written to file coords.chr17test.
419s ============================================================
419s iit.test
419s Finished reading FASTA file -- total entries: 3
419s Maximum coordinate: 40000
419s Total label length: 3 + 3 separators
419s Total annotation length: 80 + 3 separators
419s Saw 0 distinct divisions/chromosomes
419s Saw 3 distinct tags/types
419s No divs/chromosomes provided, so storing as IIT version 1
419s Writing IIT file header information...coordinates require 4 bytes each...done
419s Processing null division/chromosome...sorting...writing...done (3 intervals)
419s Writing IIT file footer information...done
419s setup1.test
419s --local flag not specified, so building localdb by default
419s Writing files under .
419s Not sorting chromosomes.  To sort chromosomes other ways, use the -s flag.
419s Creating files in directory ./chr17test
421s Running "/usr/lib/gmap/fa_coords"        -o "./chr17test.coords" -f "./chr17test.sources"
421s Opening file /tmp/tmp.Zlurl7zS3F/tests/ss.chr17test
421s   Processed short contigs (<1000000 nt): .
421s ============================================================
421s Contig mapping information has been written to file ./chr17test.coords.
421s ============================================================
423s Running "/usr/lib/gmap/gmap_process"   -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex"  -d chr17test -D "./chr17test" -A -s none
423s Reading coordinates from file ./chr17test.coords
423s Logging contig chr17test at chr17test:1..200000 in genome chr17test
423s  => primary (linear) chromosome
423s Total genomic length = 200000 bp
423s divsort == NO_SORT
423s Have a total of 1 chromosomes
423s Writing chromosome file ./chr17test/chr17test.chromosome
423s Chromosome chr17test has universal coordinates 1..200000
423s Writing chromosome IIT file ./chr17test/chr17test.chromosome.iit
423s Writing IIT file header information...coordinates require 4 bytes each...done
423s Processing null division/chromosome...sorting...writing...done (1 intervals)
423s Writing IIT file footer information...done
423s Writing IIT file header information...coordinates require 4 bytes each...done
423s Processing null division/chromosome...sorting...writing...done (1 intervals)
423s Writing IIT file footer information...done
423s No alternate scaffolds observed
425s Running "/usr/lib/gmap/gmap_process"   -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex"  -d chr17test -D "./chr17test" -G
425s Genome length is 200000 nt
425s Trying to allocate 18752*4 bytes of memory...succeeded.  Building genome in memory.
425s Reading coordinates from file ./chr17test.coords
425s Writing contig chr17test to universal coordinates 1..200000
425s A total of 0 non-ACGTNX characters were seen in the genome.
427s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -U
429s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -k 15 -q 3  -D "./chr17test" -d chr17test -N
429s Counting positions in genome chr17test (15 bp every 3 bp), position 0
429s Number of positions: 200000 => normal-sized genome
429s Number of offsets: 66662 => pages file not required
431s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3  -D "./chr17test" -d chr17test -O "./chr17test/chr17test.genomecomp"
431s Offset compression types: bitpack64
431s Allocating 16777216*1 bytes for packsizes
431s Allocating 16777216*8 bytes for bitpacks
431s Indexing offsets of oligomers in genome chr17test (15 bp every 3 bp), position 0
433s Writing 1073741825 offsets compressed via bitpack64...done
435s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3  -D "./chr17test" -d chr17test -P "./chr17test/chr17test.genomecomp"
435s Looking for genome chr17test in directory ./chr17test
435s Looking for index files in directory ./chr17test
435s   Pointers file is chr17test.ref153offsets64meta
435s   Offsets file is chr17test.ref153offsets64strm
435s   Positions file is chr17test.ref153positions
436s Expanding offsetsstrm into counters...done
436s Allocating 1004928 bytes for counterstrm
436s Trying to allocate 66662*4 bytes of memory for positions...succeeded.  Building positions in memory.
436s Indexing positions of oligomers in genome chr17test (15 bp every 3 bp), position 0
436s Writing 66662 genomic positions to file ./chr17test/chr17test.ref153positions ...
436s done
438s Running "/usr/lib/gmap/gmapindex"  -D "./chr17test" -d chr17test -Q "./chr17test/chr17test.genomecomp"
438s Writing localdb sarrays
440s autopkgtest [16:56:46]: test gmap-tests: -----------------------]
444s autopkgtest [16:56:50]: test gmap-tests:  - - - - - - - - - - results - - - - - - - - - -
444s gmap-tests           PASS
445s autopkgtest [16:56:51]: @@@@@@@@@@@@@@@@@@@@ summary
445s gmap-tests           PASS
477s nova [W] Skipping flock in bos03-arm64
477s Creating nova instance adt-oracular-arm64-gmap-20240712-164925-juju-7f2275-prod-proposed-migration-environment-3-b74d5e35-dcfa-443f-bc9a-e109ef594fd7 from image adt/ubuntu-oracular-arm64-server-20240712.img (UUID a9c53646-2a41-49d7-a14b-d40262a2cb6c)...