0s autopkgtest [17:46:02]: starting date and time: 2024-03-24 17:46:02+0000 0s autopkgtest [17:46:02]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:46:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yefl8dyu/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade snpomatic --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 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-2@bos02-arm64-4.secgroup --name adt-noble-arm64-snpomatic-20240324-174602-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://ftpmaster.internal/ubuntu/ 226s autopkgtest [17:49:48]: testbed dpkg architecture: arm64 226s autopkgtest [17:49:48]: testbed apt version: 2.7.12 226s autopkgtest [17:49:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 228s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 229s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 229s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 229s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 230s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 230s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 230s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 230s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 230s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 230s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 231s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 231s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 231s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 244s Fetched 9851 kB in 6s (1561 kB/s) 245s Reading package lists... 253s Reading package lists... 254s Building dependency tree... 254s Reading state information... 256s Calculating upgrade... 258s The following packages will be REMOVED: 258s libssl3 258s The following NEW packages will be installed: 258s libssl3t64 258s The following packages have been kept back: 258s curl 258s The following packages will be upgraded: 258s openssl 258s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 258s Need to get 2777 kB of archives. 258s After this operation, 139 kB of additional disk space will be used. 258s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 259s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 261s Fetched 2777 kB in 2s (1709 kB/s) 262s (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.) 262s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 262s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 263s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 263s wget depends on libssl3 (>= 3.0.0). 263s u-boot-tools depends on libssl3 (>= 3.0.0). 263s tnftp depends on libssl3 (>= 3.0.0). 263s tcpdump depends on libssl3 (>= 3.0.0). 263s systemd-resolved depends on libssl3 (>= 3.0.0). 263s systemd depends on libssl3 (>= 3.0.0). 263s sudo depends on libssl3 (>= 3.0.0). 263s sbsigntool depends on libssl3 (>= 3.0.0). 263s rsync depends on libssl3 (>= 3.0.0). 263s python3-cryptography depends on libssl3 (>= 3.0.0). 263s openssh-server depends on libssl3 (>= 3.0.10). 263s openssh-client depends on libssl3 (>= 3.0.10). 263s mtd-utils depends on libssl3 (>= 3.0.0). 263s mokutil depends on libssl3 (>= 3.0.0). 263s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 263s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 263s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 263s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 263s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 263s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 263s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 263s libnvme1 depends on libssl3 (>= 3.0.0). 263s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 263s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 263s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 263s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 263s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 263s kmod depends on libssl3 (>= 3.0.0). 263s dhcpcd-base depends on libssl3 (>= 3.0.0). 263s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 263s 263s (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.) 263s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 263s Selecting previously unselected package libssl3t64:arm64. 264s (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.) 264s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 264s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 264s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 264s Setting up openssl (3.0.13-0ubuntu2) ... 264s Processing triggers for man-db (2.12.0-3) ... 266s Processing triggers for libc-bin (2.39-0ubuntu6) ... 268s Reading package lists... 269s Building dependency tree... 269s Reading state information... 271s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 274s sh: Attempting to set up Debian/Ubuntu apt sources automatically 274s sh: Distribution appears to be Ubuntu 277s Reading package lists... 278s Building dependency tree... 278s Reading state information... 281s eatmydata is already the newest version (131-1). 281s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 281s Reading package lists... 281s Building dependency tree... 281s Reading state information... 284s dbus is already the newest version (1.14.10-4ubuntu1). 284s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 284s Reading package lists... 286s Building dependency tree... 286s Reading state information... 289s rng-tools-debian is already the newest version (2.4). 289s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 290s Reading package lists... 291s Building dependency tree... 291s Reading state information... 294s The following packages will be REMOVED: 294s cloud-init* python3-configobj* python3-debconf* 296s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 296s After this operation, 3256 kB disk space will be freed. 296s (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.) 296s Removing cloud-init (24.1.2-0ubuntu1) ... 301s Removing python3-configobj (5.0.8-3) ... 301s Removing python3-debconf (1.5.86) ... 302s Processing triggers for man-db (2.12.0-3) ... 303s (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.) 303s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 308s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 308s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 308s invoke-rc.d: policy-rc.d denied execution of try-restart. 309s Reading package lists... 310s Building dependency tree... 310s Reading state information... 313s linux-generic is already the newest version (6.8.0-11.11+1). 313s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 314s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 314s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 314s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 326s Reading package lists... 326s Reading package lists... 327s Building dependency tree... 327s Reading state information... 329s Calculating upgrade... 331s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 331s Reading package lists... 332s Building dependency tree... 332s Reading state information... 334s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 334s autopkgtest [17:51:36]: rebooting testbed after setup commands that affected boot 515s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 524s autopkgtest [17:54:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 528s autopkgtest [17:54:50]: @@@@@@@@@@@@@@@@@@@@ apt-source snpomatic 533s Get:1 http://ftpmaster.internal/ubuntu noble/universe snpomatic 1.0-7 (dsc) [1990 B] 533s Get:2 http://ftpmaster.internal/ubuntu noble/universe snpomatic 1.0-7 (tar) [66.5 kB] 533s Get:3 http://ftpmaster.internal/ubuntu noble/universe snpomatic 1.0-7 (diff) [9876 B] 534s gpgv: Signature made Sat Dec 23 08:22:17 2023 UTC 534s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 534s gpgv: Can't check signature: No public key 534s dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found 534s autopkgtest [17:54:56]: testing package snpomatic version 1.0-7 534s autopkgtest [17:54:56]: build not needed 535s autopkgtest [17:54:57]: test test-example: preparing testbed 537s Reading package lists... 538s Building dependency tree... 538s Reading state information... 539s Starting pkgProblemResolver with broken count: 0 539s Starting 2 pkgProblemResolver with broken count: 0 539s Done 541s The following additional packages will be installed: 541s libdeflate0 libhts3 libhtscodecs2 samtools snpomatic 541s Suggested packages: 541s cwltool 541s The following NEW packages will be installed: 541s autopkgtest-satdep libdeflate0 libhts3 libhtscodecs2 samtools snpomatic 542s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 542s Need to get 1206 kB/1207 kB of archives. 542s After this operation, 3259 kB of additional disk space will be used. 542s Get:1 /tmp/autopkgtest.8YS1dp/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 542s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 542s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 542s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 543s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 543s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 snpomatic arm64 1.0-7 [78.4 kB] 545s Fetched 1206 kB in 2s (764 kB/s) 545s Selecting previously unselected package libdeflate0:arm64. 545s (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.) 546s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ... 546s Unpacking libdeflate0:arm64 (1.19-1) ... 546s Selecting previously unselected package libhtscodecs2:arm64. 546s Preparing to unpack .../1-libhtscodecs2_1.6.0-1_arm64.deb ... 546s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 546s Selecting previously unselected package libhts3:arm64. 546s Preparing to unpack .../2-libhts3_1.18+ds-1_arm64.deb ... 546s Unpacking libhts3:arm64 (1.18+ds-1) ... 546s Selecting previously unselected package samtools. 546s Preparing to unpack .../3-samtools_1.19.2-1_arm64.deb ... 546s Unpacking samtools (1.19.2-1) ... 546s Selecting previously unselected package snpomatic. 546s Preparing to unpack .../4-snpomatic_1.0-7_arm64.deb ... 546s Unpacking snpomatic (1.0-7) ... 546s Selecting previously unselected package autopkgtest-satdep. 546s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 546s Unpacking autopkgtest-satdep (0) ... 546s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 546s Setting up libdeflate0:arm64 (1.19-1) ... 546s Setting up snpomatic (1.0-7) ... 547s Setting up libhts3:arm64 (1.18+ds-1) ... 547s Setting up samtools (1.19.2-1) ... 547s Setting up autopkgtest-satdep (0) ... 547s Processing triggers for man-db (2.12.0-3) ... 549s Processing triggers for libc-bin (2.39-0ubuntu6) ... 558s (Reading database ... 75585 files and directories currently installed.) 558s Removing autopkgtest-satdep (0) ... 559s autopkgtest [17:55:21]: test test-example: [----------------------- 560s [wgsim] seed = 42 560s [wgsim_core] calculating the total length of the reference sequence... 560s [wgsim_core] 1 sequences, total length: 11940 560s ref 134 C Y + 560s ref 137 G C - 560s ref 213 A R + 560s ref 276 - A + 560s ref 320 T W + 560s ref 469 A C - 560s ref 631 G T - 560s ref 678 - TTT - 560s ref 682 G K + 560s ref 796 GA - - 560s ref 974 C G - 560s ref 1056 A R + 560s ref 1156 A G - 560s ref 1170 G S + 560s ref 1298 C M + 560s ref 1326 G K + 560s ref 1343 T A - 560s ref 1422 G - - 560s ref 1639 T Y + 560s ref 1722 T G - 560s ref 2008 C M + 560s ref 2060 T K + 560s ref 2103 - G + 560s ref 2179 C M + 560s ref 2322 A M + 560s ref 2328 A W + 560s ref 2381 A T - 560s ref 2560 C Y + 560s ref 2618 G C - 560s ref 2833 - CG - 560s ref 2944 G K + 560s ref 2978 T C - 560s ref 2984 G R + 560s ref 2988 C M + 560s ref 3017 C S + 560s ref 3038 G C - 560s ref 3358 G S + 560s ref 3443 G A - 560s ref 3558 G R + 560s ref 3559 A R + 560s ref 3765 G R + 560s ref 3863 C M + 560s ref 4101 G T - 560s ref 4271 G S + 560s ref 4475 G K + 560s ref 4690 G S + 560s ref 4730 G C - 560s ref 4735 G K + 560s ref 4917 C G - 560s ref 4983 A G - 560s ref 5178 A R + 560s ref 5307 T G - 560s ref 5365 ACA - - 560s ref 5403 G S + 560s ref 5411 T C - 560s ref 5434 C S + 560s ref 5465 G - - 560s ref 5507 T Y + 560s ref 5544 A R + 560s ref 5588 - T - 560s ref 5702 A M + 560s ref 6146 T K + 560s ref 6158 G A - 560s ref 6181 G A - 560s ref 6207 A W + 560s ref 6216 T A - 560s ref 6286 T K + 560s ref 6346 GC - - 560s ref 6697 G S + 560s ref 6745 C S + 560s ref 6754 T C - 560s ref 6818 G R + 560s ref 6922 C T - 560s ref 7123 C A - 560s ref 7644 C Y + 560s ref 7699 T Y + 560s ref 7793 C T - 560s ref 7861 C T - 560s ref 7877 G C - 560s ref 7970 T G - 560s ref 7973 A G - 560s ref 8068 T W + 560s ref 8157 G C - 560s ref 8164 G R + 560s ref 8442 G K + 560s ref 8483 A R + 560s ref 8498 C Y + 560s ref 8532 A M + 560s ref 8721 C Y + 560s ref 9084 G - - 560s ref 9192 G T - 560s ref 9208 C A - 560s ref 9211 G S + 560s ref 9341 C Y + 560s ref 9372 T K + 560s ref 9393 - C + 560s ref 9597 A C - 560s ref 9621 AC - - 560s ref 9739 C A - 560s ref 9790 CATC - - 560s ref 9881 A C - 560s ref 9902 A G - 560s ref 10134 T G - 560s ref 10212 G C - 560s ref 10214 G K + 560s ref 10556 - TA - 560s ref 10751 T W + 560s ref 10777 C S + 560s ref 10799 C Y + 560s ref 10832 C S + 560s ref 10858 A G - 560s ref 11015 C Y + 560s ref 11038 C Y + 560s ref 11108 C Y + 560s ref 11179 A M + 560s ref 11217 G R + 560s ref 11275 C M + 560s ref 11290 C S + 560s ref 11481 G - - 560s ref 11566 T G - 560s ref 11655 A G - 560s ref 11771 G T - 560s Reading all chromosomes from ref.fasta ... read 1 chromosomes. 560s Indexing 1 chromosomes ... sorting ... done. 560s Setting read length to 70 560s Reading solexa pair data from reads.1.fq ... scanned 10000 solexa reads, 222 (2.22%) matched , 222 total matches, 0 skipped. 561s autopkgtest [17:55:23]: test test-example: -----------------------] 561s autopkgtest [17:55:23]: test test-example: - - - - - - - - - - results - - - - - - - - - - 561s test-example PASS 562s autopkgtest [17:55:24]: @@@@@@@@@@@@@@@@@@@@ summary 562s test-example PASS 609s Creating nova instance adt-noble-arm64-snpomatic-20240324-174602-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...