0s autopkgtest [14:30:10]: starting date and time: 2024-07-12 14:30:10+0000 1s autopkgtest [14:30:11]: git checkout: fd3bed09 nova: allow more retries for quota issues 1s autopkgtest [14:30:11]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.b07wfoca/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@lcy02-1.secgroup --name adt-oracular-amd64-gmap-20240712-143010-juju-7f2275-prod-proposed-migration-environment-3-16feb900-1608-4757-b219-3828fa5bb39d --image adt/ubuntu-oracular-amd64-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/ 155s autopkgtest [14:32:45]: testbed dpkg architecture: amd64 155s autopkgtest [14:32:45]: testbed apt version: 2.9.6 155s autopkgtest [14:32:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 156s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 156s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [344 kB] 156s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [43.3 kB] 156s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 156s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 156s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [70.7 kB] 156s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [97.7 kB] 156s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B] 156s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 156s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 156s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 156s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [244 kB] 156s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [387 kB] 156s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B] 156s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 156s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 156s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 157s Fetched 1387 kB in 0s (5385 kB/s) 157s Reading package lists... 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s Calculating upgrade... 163s The following packages will be upgraded: 163s binutils binutils-common binutils-x86-64-linux-gnu gir1.2-glib-2.0 163s libbinutils libc-bin libc-dev-bin libc-devtools libc6 libc6-dev 163s libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data libgprofng0 163s libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssh-client 163s openssh-server openssh-sftp-server openssl 163s 24 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 22.7 MB of archives. 163s After this operation, 428 kB of additional disk space will be used. 163s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB] 163s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB] 163s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB] 163s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB] 163s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB] 163s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.2.2-1ubuntu1 [2138 kB] 163s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-sftp-server amd64 1:9.6p1-3ubuntu17 [37.1 kB] 163s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-server amd64 1:9.6p1-3ubuntu17 [509 kB] 163s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 openssh-client amd64 1:9.6p1-3ubuntu17 [905 kB] 163s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.4-1ubuntu1 [182 kB] 163s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.4-1ubuntu1 [1545 kB] 163s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB] 163s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB] 163s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.2.2-1ubuntu1 [1122 kB] 163s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.62.1-2 [75.1 kB] 163s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42.50.20240710-1ubuntu1 [860 kB] 163s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42.50.20240710-1ubuntu1 [95.6 kB] 163s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42.50.20240710-1ubuntu1 [97.6 kB] 163s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240710-1ubuntu1 [2477 kB] 164s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42.50.20240710-1ubuntu1 [574 kB] 164s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42.50.20240710-1ubuntu1 [18.1 kB] 164s Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42.50.20240710-1ubuntu1 [243 kB] 164s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42.50.20240710-1ubuntu1 [14.4 kB] 164s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libnss3 amd64 2:3.102-1 [1399 kB] 164s Preconfiguring packages ... 164s Fetched 22.7 MB in 0s (45.4 MB/s) 164s (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 ... 74487 files and directories currently installed.) 164s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ... 164s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 164s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ... 164s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 164s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ... 164s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 165s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ... 165s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 165s Setting up libc6:amd64 (2.39-3.1ubuntu3) ... 165s Error: Could not restart systemd, systemd binary not working 165s (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 ... 74487 files and directories currently installed.) 165s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ... 165s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 165s Setting up libc-bin (2.39-3.1ubuntu3) ... 165s (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 ... 74487 files and directories currently installed.) 165s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_amd64.deb ... 165s Unpacking libssl3t64:amd64 (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 165s Setting up libssl3t64:amd64 (3.2.2-1ubuntu1) ... 165s (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 ... 74487 files and directories currently installed.) 165s Preparing to unpack .../00-openssh-sftp-server_1%3a9.6p1-3ubuntu17_amd64.deb ... 165s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 165s Preparing to unpack .../01-openssh-server_1%3a9.6p1-3ubuntu17_amd64.deb ... 165s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 166s Preparing to unpack .../02-openssh-client_1%3a9.6p1-3ubuntu17_amd64.deb ... 166s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 166s Preparing to unpack .../03-gir1.2-glib-2.0_2.80.4-1ubuntu1_amd64.deb ... 166s Unpacking gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 166s Preparing to unpack .../04-libglib2.0-0t64_2.80.4-1ubuntu1_amd64.deb ... 166s Unpacking libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 166s Preparing to unpack .../05-libglib2.0-data_2.80.4-1ubuntu1_all.deb ... 166s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 166s Preparing to unpack .../06-locales_2.39-3.1ubuntu3_all.deb ... 166s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 166s Preparing to unpack .../07-openssl_3.2.2-1ubuntu1_amd64.deb ... 166s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 166s Preparing to unpack .../08-libnghttp2-14_1.62.1-2_amd64.deb ... 166s Unpacking libnghttp2-14:amd64 (1.62.1-2) over (1.62.1-1) ... 166s Preparing to unpack .../09-libgprofng0_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../10-libctf0_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking libctf0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../11-libctf-nobfd0_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../12-binutils-x86-64-linux-gnu_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../13-libbinutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking libbinutils:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../14-binutils_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../15-binutils-common_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking binutils-common:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 166s Preparing to unpack .../16-libsframe1_2.42.50.20240710-1ubuntu1_amd64.deb ... 166s Unpacking libsframe1:amd64 (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 167s Preparing to unpack .../17-libnss3_2%3a3.102-1_amd64.deb ... 167s Unpacking libnss3:amd64 (2:3.102-1) over (2:3.101-1) ... 167s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 167s Setting up binutils-common:amd64 (2.42.50.20240710-1ubuntu1) ... 167s Setting up libnghttp2-14:amd64 (1.62.1-2) ... 167s Setting up libctf-nobfd0:amd64 (2.42.50.20240710-1ubuntu1) ... 167s Setting up libnss3:amd64 (2:3.102-1) ... 167s Setting up locales (2.39-3.1ubuntu3) ... 167s Generating locales (this might take a while)... 169s en_US.UTF-8... done 169s Generation complete. 169s Setting up libsframe1:amd64 (2.42.50.20240710-1ubuntu1) ... 169s Setting up libglib2.0-0t64:amd64 (2.80.4-1ubuntu1) ... 169s No schema files found: doing nothing. 169s Setting up libglib2.0-data (2.80.4-1ubuntu1) ... 169s Setting up gir1.2-glib-2.0:amd64 (2.80.4-1ubuntu1) ... 169s Setting up libbinutils:amd64 (2.42.50.20240710-1ubuntu1) ... 169s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 169s Setting up openssl (3.2.2-1ubuntu1) ... 169s Installing new version of config file /etc/ssl/openssl.cnf ... 169s Setting up libc-devtools (2.39-3.1ubuntu3) ... 169s Setting up libctf0:amd64 (2.42.50.20240710-1ubuntu1) ... 169s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 169s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 169s Installing new version of config file /etc/pam.d/sshd ... 170s Setting up libgprofng0:amd64 (2.42.50.20240710-1ubuntu1) ... 170s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ... 170s Setting up binutils-x86-64-linux-gnu (2.42.50.20240710-1ubuntu1) ... 170s Setting up binutils (2.42.50.20240710-1ubuntu1) ... 170s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 170s Processing triggers for ufw (0.36.2-6) ... 170s Processing triggers for systemd (256-1ubuntu1) ... 171s Processing triggers for man-db (2.12.1-2) ... 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 173s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 173s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 173s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 175s Reading package lists... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Calculating upgrade... 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s autopkgtest [14:33:07]: rebooting testbed after setup commands that affected boot 180s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 192s autopkgtest [14:33:22]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 194s autopkgtest [14:33:24]: @@@@@@@@@@@@@@@@@@@@ apt-source gmap 196s Get:1 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (dsc) [2191 B] 196s Get:2 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (tar) [2495 kB] 196s Get:3 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (diff) [13.3 kB] 196s gpgv: Signature made Sun May 26 10:21:41 2024 UTC 196s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 196s gpgv: issuer "emollier@debian.org" 196s gpgv: Can't check signature: No public key 196s dpkg-source: warning: cannot verify inline signature for ./gmap_2024-05-20+ds-1.dsc: no acceptable signature found 196s autopkgtest [14:33:26]: testing package gmap version 2024-05-20+ds-1 202s autopkgtest [14:33:32]: build not needed 210s autopkgtest [14:33:40]: test gmap-tests: preparing testbed 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 213s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 214s The following additional packages will be installed: 214s gmap 214s The following NEW packages will be installed: 214s autopkgtest-satdep gmap 214s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 214s Need to get 21.9 MB/21.9 MB of archives. 214s After this operation, 221 MB of additional disk space will be used. 214s Get:1 /tmp/autopkgtest.h48rdJ/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 214s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 gmap amd64 2024-05-20+ds-1 [21.9 MB] 215s Fetched 21.9 MB in 1s (27.6 MB/s) 215s Selecting previously unselected package gmap. 215s (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 ... 74486 files and directories currently installed.) 215s Preparing to unpack .../gmap_2024-05-20+ds-1_amd64.deb ... 215s Unpacking gmap (2024-05-20+ds-1) ... 216s Selecting previously unselected package autopkgtest-satdep. 216s Preparing to unpack .../1-autopkgtest-satdep.deb ... 216s Unpacking autopkgtest-satdep (0) ... 216s Setting up gmap (2024-05-20+ds-1) ... 216s Setting up autopkgtest-satdep (0) ... 216s Processing triggers for man-db (2.12.1-2) ... 232s (Reading database ... 74597 files and directories currently installed.) 232s Removing autopkgtest-satdep (0) ... 233s autopkgtest [14:34:03]: test gmap-tests: [----------------------- 240s align.test 240s GMAP version 2024-05-20 called with args: gmap.avx2 -A -g /tmp/tmp.ld3ExwSElJ/tests/ss.chr17test /tmp/tmp.ld3ExwSElJ/tests/ss.her2 240s Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1 240s Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends 240s Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17 240s Finished checking compiler assumptions 240s Starting alignment 240s Processed 1 queries in 0.04 seconds (24.41 queries/sec) 240s coords1.test 240s Opening file /tmp/tmp.ld3ExwSElJ/tests/ss.chr17test 240s Processed short contigs (<1000000 nt): . 240s ============================================================ 240s Contig mapping information has been written to file coords.chr17test. 240s ============================================================ 240s iit.test 240s Finished reading FASTA file -- total entries: 3 240s Maximum coordinate: 40000 240s Total label length: 3 + 3 separators 240s Total annotation length: 80 + 3 separators 240s Saw 0 distinct divisions/chromosomes 240s Saw 3 distinct tags/types 240s No divs/chromosomes provided, so storing as IIT version 1 240s Writing IIT file header information...coordinates require 4 bytes each...done 240s Processing null division/chromosome...sorting...writing...done (3 intervals) 240s Writing IIT file footer information...done 240s setup1.test 240s --local flag not specified, so building localdb by default 240s Writing files under . 240s Not sorting chromosomes. To sort chromosomes other ways, use the -s flag. 240s Creating files in directory ./chr17test 242s Running "/usr/lib/gmap/fa_coords" -o "./chr17test.coords" -f "./chr17test.sources" 242s Opening file /tmp/tmp.ld3ExwSElJ/tests/ss.chr17test 242s Processed short contigs (<1000000 nt): . 242s ============================================================ 242s Contig mapping information has been written to file ./chr17test.coords. 242s ============================================================ 244s Running "/usr/lib/gmap/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -A -s none 244s Reading coordinates from file ./chr17test.coords 244s Logging contig chr17test at chr17test:1..200000 in genome chr17test 244s => primary (linear) chromosome 244s Total genomic length = 200000 bp 244s divsort == NO_SORT 244s Have a total of 1 chromosomes 244s Writing chromosome file ./chr17test/chr17test.chromosome 244s Chromosome chr17test has universal coordinates 1..200000 244s Writing chromosome IIT file ./chr17test/chr17test.chromosome.iit 244s Writing IIT file header information...coordinates require 4 bytes each...done 244s Processing null division/chromosome...sorting...writing...done (1 intervals) 244s Writing IIT file footer information...done 244s Writing IIT file header information...coordinates require 4 bytes each...done 244s Processing null division/chromosome...sorting...writing...done (1 intervals) 244s Writing IIT file footer information...done 244s No alternate scaffolds observed 246s Running "/usr/lib/gmap/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -G 246s Genome length is 200000 nt 246s Trying to allocate 18752*4 bytes of memory...succeeded. Building genome in memory. 246s Reading coordinates from file ./chr17test.coords 246s Writing contig chr17test to universal coordinates 1..200000 246s A total of 0 non-ACGTNX characters were seen in the genome. 248s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -U 250s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -N 250s Counting positions in genome chr17test (15 bp every 3 bp), position 0 250s Number of positions: 200000 => normal-sized genome 250s Number of offsets: 66662 => pages file not required 252s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -O "./chr17test/chr17test.genomecomp" 252s Offset compression types: bitpack64 252s Allocating 16777216*1 bytes for packsizes 252s Allocating 16777216*8 bytes for bitpacks 252s Indexing offsets of oligomers in genome chr17test (15 bp every 3 bp), position 0 254s Writing 1073741825 offsets compressed via bitpack64...done 256s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -P "./chr17test/chr17test.genomecomp" 256s Looking for genome chr17test in directory ./chr17test 256s Looking for index files in directory ./chr17test 256s Pointers file is chr17test.ref153offsets64meta 256s Offsets file is chr17test.ref153offsets64strm 256s Positions file is chr17test.ref153positions 256s Expanding offsetsstrm into counters...done 256s Allocating 1004928 bytes for counterstrm 256s Trying to allocate 66662*4 bytes of memory for positions...succeeded. Building positions in memory. 256s Indexing positions of oligomers in genome chr17test (15 bp every 3 bp), position 0 256s Writing 66662 genomic positions to file ./chr17test/chr17test.ref153positions ... 256s done 258s Running "/usr/lib/gmap/gmapindex" -D "./chr17test" -d chr17test -Q "./chr17test/chr17test.genomecomp" 258s Writing localdb sarrays 261s autopkgtest [14:34:31]: test gmap-tests: -----------------------] 261s autopkgtest [14:34:31]: test gmap-tests: - - - - - - - - - - results - - - - - - - - - - 261s gmap-tests PASS 261s autopkgtest [14:34:31]: @@@@@@@@@@@@@@@@@@@@ summary 261s gmap-tests PASS 277s nova [W] Skipping flock for amd64 277s Creating nova instance adt-oracular-amd64-gmap-20240712-143010-juju-7f2275-prod-proposed-migration-environment-3-16feb900-1608-4757-b219-3828fa5bb39d from image adt/ubuntu-oracular-amd64-server-20240711.img (UUID 4d65b1cc-a829-44fc-a8ac-cdd52093f9db)...