0s autopkgtest [13:02:51]: starting date and time: 2024-07-13 13:02:51+0000 0s autopkgtest [13:02:51]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [13:02:51]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.aa7mr7mz/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.171 lxd-armhf-10.145.243.171:autopkgtest/ubuntu/oracular/armhf 65s autopkgtest [13:03:56]: testbed dpkg architecture: armhf 67s autopkgtest [13:03:58]: testbed apt version: 2.9.6 67s autopkgtest [13:03:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 78s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 78s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [49.0 kB] 78s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 78s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [363 kB] 78s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [77.6 kB] 78s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf c-n-f Metadata [1428 B] 78s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf Packages [1368 B] 78s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf c-n-f Metadata [120 B] 78s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [349 kB] 78s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf c-n-f Metadata [6916 B] 78s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1448 B] 78s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf c-n-f Metadata [120 B] 80s Fetched 987 kB in 3s (380 kB/s) 80s Reading package lists... 98s tee: /proc/self/fd/2: Permission denied 122s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 122s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 122s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 122s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 124s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Calculating upgrade... 126s The following packages will be upgraded: 126s libc-bin libc6 locales 126s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 7572 kB of archives. 126s After this operation, 17.4 kB of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc6 armhf 2.39-3.1ubuntu3 [2825 kB] 126s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc-bin armhf 2.39-3.1ubuntu3 [527 kB] 126s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf locales all 2.39-3.1ubuntu3 [4220 kB] 127s Preconfiguring packages ... 128s Fetched 7572 kB in 1s (8979 kB/s) 128s (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 ... 58436 files and directories currently installed.) 128s Preparing to unpack .../libc6_2.39-3.1ubuntu3_armhf.deb ... 128s Unpacking libc6:armhf (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 128s Setting up libc6:armhf (2.39-3.1ubuntu3) ... 128s Error: Could not restart systemd, systemd binary not working 128s (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 ... 58436 files and directories currently installed.) 128s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_armhf.deb ... 128s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 128s Setting up libc-bin (2.39-3.1ubuntu3) ... 129s (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 ... 58436 files and directories currently installed.) 129s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 129s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 129s Setting up locales (2.39-3.1ubuntu3) ... 130s Generating locales (this might take a while)... 132s en_US.UTF-8... done 133s Generation complete. 133s Processing triggers for systemd (256-1ubuntu1) ... 134s Processing triggers for man-db (2.12.1-2) ... 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s autopkgtest [13:05:10]: rebooting testbed after setup commands that affected boot 210s autopkgtest [13:06:21]: testbed running kernel: Linux 6.5.0-35-generic #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May 7 11:19:33 UTC 2 238s autopkgtest [13:06:49]: @@@@@@@@@@@@@@@@@@@@ apt-source gmap 250s Get:1 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (dsc) [2191 B] 250s Get:2 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (tar) [2495 kB] 250s Get:3 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (diff) [13.3 kB] 251s gpgv: Signature made Sun May 26 10:21:41 2024 UTC 251s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 251s gpgv: issuer "emollier@debian.org" 251s gpgv: Can't check signature: No public key 251s dpkg-source: warning: cannot verify inline signature for ./gmap_2024-05-20+ds-1.dsc: no acceptable signature found 251s autopkgtest [13:07:02]: testing package gmap version 2024-05-20+ds-1 253s autopkgtest [13:07:04]: build not needed 256s autopkgtest [13:07:07]: test gmap-tests: preparing testbed 266s Reading package lists... 266s Building dependency tree... 266s Reading state information... 267s Starting pkgProblemResolver with broken count: 0 267s Starting 2 pkgProblemResolver with broken count: 0 267s Done 268s The following additional packages will be installed: 268s gmap 268s The following NEW packages will be installed: 268s autopkgtest-satdep gmap 268s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 268s Need to get 5566 kB/5566 kB of archives. 268s After this operation, 42.8 MB of additional disk space will be used. 268s Get:1 /tmp/autopkgtest.K1pMg5/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [700 B] 268s Get:2 http://ftpmaster.internal/ubuntu oracular/universe armhf gmap armhf 2024-05-20+ds-1 [5566 kB] 269s Fetched 5566 kB in 1s (7301 kB/s) 269s Selecting previously unselected package gmap. 269s (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 ... 58436 files and directories currently installed.) 269s Preparing to unpack .../gmap_2024-05-20+ds-1_armhf.deb ... 269s Unpacking gmap (2024-05-20+ds-1) ... 269s Selecting previously unselected package autopkgtest-satdep. 269s Preparing to unpack .../1-autopkgtest-satdep.deb ... 269s Unpacking autopkgtest-satdep (0) ... 269s Setting up gmap (2024-05-20+ds-1) ... 269s Setting up autopkgtest-satdep (0) ... 269s Processing triggers for man-db (2.12.1-2) ... 282s (Reading database ... 58499 files and directories currently installed.) 282s Removing autopkgtest-satdep (0) ... 288s autopkgtest [13:07:39]: test gmap-tests: [----------------------- 290s align.test 290s GMAP version 2024-05-20 called with args: gmap.nosimd -A -g /tmp/tmp.AhhRysqmeD/tests/ss.chr17test /tmp/tmp.AhhRysqmeD/tests/ss.her2 290s Finished checking compiler assumptions 290s Starting alignment 290s Processed 1 queries in 0.04 seconds (22.67 queries/sec) 290s coords1.test 290s Opening file /tmp/tmp.AhhRysqmeD/tests/ss.chr17test 290s Processed short contigs (<1000000 nt): . 290s ============================================================ 290s Contig mapping information has been written to file coords.chr17test. 290s ============================================================ 290s iit.test 290s Finished reading FASTA file -- total entries: 3 290s Maximum coordinate: 40000 290s Total label length: 3 + 3 separators 290s Total annotation length: 80 + 3 separators 290s Saw 0 distinct divisions/chromosomes 290s Saw 3 distinct tags/types 290s No divs/chromosomes provided, so storing as IIT version 1 290s Writing IIT file header information...coordinates require 4 bytes each...done 290s Processing null division/chromosome...sorting...writing...done (3 intervals) 290s Writing IIT file footer information...done 290s setup1.test 290s --local flag not specified, so building localdb by default 290s Writing files under . 290s Not sorting chromosomes. To sort chromosomes other ways, use the -s flag. 290s Creating files in directory ./chr17test 292s Running "/usr/lib/gmap/fa_coords" -o "./chr17test.coords" -f "./chr17test.sources" 292s Opening file /tmp/tmp.AhhRysqmeD/tests/ss.chr17test 292s Processed short contigs (<1000000 nt): . 292s ============================================================ 292s Contig mapping information has been written to file ./chr17test.coords. 292s ============================================================ 294s Running "/usr/lib/gmap/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -A -s none 294s Reading coordinates from file ./chr17test.coords 294s Logging contig chr17test at chr17test:1..200000 in genome chr17test 294s => primary (linear) chromosome 294s Total genomic length = 200000 bp 294s divsort == NO_SORT 294s Have a total of 1 chromosomes 294s Writing chromosome file ./chr17test/chr17test.chromosome 294s Chromosome chr17test has universal coordinates 1..200000 294s Writing chromosome IIT file ./chr17test/chr17test.chromosome.iit 294s Writing IIT file header information...coordinates require 4 bytes each...done 294s Processing null division/chromosome...sorting...writing...done (1 intervals) 294s Writing IIT file footer information...done 294s Writing IIT file header information...coordinates require 4 bytes each...done 294s Processing null division/chromosome...sorting...writing...done (1 intervals) 294s Writing IIT file footer information...done 294s No alternate scaffolds observed 296s Running "/usr/lib/gmap/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -G 296s Genome length is 200000 nt 296s Trying to allocate 18752*4 bytes of memory...succeeded. Building genome in memory. 296s Reading coordinates from file ./chr17test.coords 296s Writing contig chr17test to universal coordinates 1..200000 296s A total of 0 non-ACGTNX characters were seen in the genome. 298s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -U 300s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -N 300s Counting positions in genome chr17test (15 bp every 3 bp), position 0 300s Number of positions: 200000 => normal-sized genome 300s Number of offsets: 66662 => pages file not required 302s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -O "./chr17test/chr17test.genomecomp" 302s Offset compression types: bitpack64 302s Allocating 16777216*1 bytes for packsizes 302s Allocating 16777216*4 bytes for bitpacks 302s Indexing offsets of oligomers in genome chr17test (15 bp every 3 bp), position 0 305s Writing 1073741825 offsets compressed via bitpack64...done 308s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -P "./chr17test/chr17test.genomecomp" 308s Looking for genome chr17test in directory ./chr17test 308s Looking for index files in directory ./chr17test 308s Pointers file is chr17test.ref153offsets64meta 308s Offsets file is chr17test.ref153offsets64strm 308s Positions file is chr17test.ref153positions 308s Expanding offsetsstrm into counters...done 308s Allocating 1004928 bytes for counterstrm 308s Trying to allocate 66662*4 bytes of memory for positions...succeeded. Building positions in memory. 308s Indexing positions of oligomers in genome chr17test (15 bp every 3 bp), position 0 308s Writing 66662 genomic positions to file ./chr17test/chr17test.ref153positions ... 308s done 310s Running "/usr/lib/gmap/gmapindex" -D "./chr17test" -d chr17test -Q "./chr17test/chr17test.genomecomp" 310s Writing localdb sarrays 312s autopkgtest [13:08:03]: test gmap-tests: -----------------------] 317s autopkgtest [13:08:07]: test gmap-tests: - - - - - - - - - - results - - - - - - - - - - 317s gmap-tests PASS 321s autopkgtest [13:08:12]: @@@@@@@@@@@@@@@@@@@@ summary 321s gmap-tests PASS