0s autopkgtest [17:14:34]: starting date and time: 2024-03-16 17:14:34+0000 0s autopkgtest [17:14:34]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:14:34]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q8po2xt5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade rna-star --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- 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-rna-star-20240316-171434-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/ 187s autopkgtest [17:17:41]: testbed dpkg architecture: arm64 187s autopkgtest [17:17:41]: testbed apt version: 2.7.12 187s autopkgtest [17:17:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 190s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 191s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 191s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 191s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 191s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 192s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 192s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 192s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 192s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 192s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 193s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 193s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 193s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 208s Fetched 9063 kB in 8s (1176 kB/s) 209s Reading package lists... 218s Reading package lists... 219s Building dependency tree... 219s Reading state information... 222s Calculating upgrade... 224s The following packages will be REMOVED: 224s libssl3 224s The following NEW packages will be installed: 224s libssl3t64 224s The following packages have been kept back: 224s curl 224s The following packages will be upgraded: 224s openssl 224s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 224s Need to get 2753 kB of archives. 224s After this operation, 72.7 kB of additional disk space will be used. 224s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 225s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 227s Fetched 2753 kB in 1s (2819 kB/s) 229s (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 ... 75850 files and directories currently installed.) 229s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 229s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 231s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 231s wget depends on libssl3 (>= 3.0.0). 231s u-boot-tools depends on libssl3 (>= 3.0.0). 231s tnftp depends on libssl3 (>= 3.0.0). 231s tcpdump depends on libssl3 (>= 3.0.0). 231s systemd-resolved depends on libssl3 (>= 3.0.0). 231s systemd depends on libssl3 (>= 3.0.0). 231s sudo depends on libssl3 (>= 3.0.0). 231s sbsigntool depends on libssl3 (>= 3.0.0). 231s rsync depends on libssl3 (>= 3.0.0). 231s python3-cryptography depends on libssl3 (>= 3.0.0). 231s openssh-server depends on libssl3 (>= 3.0.10). 231s openssh-client depends on libssl3 (>= 3.0.10). 231s mtd-utils depends on libssl3 (>= 3.0.0). 231s mokutil depends on libssl3 (>= 3.0.0). 231s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 231s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 231s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 231s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 231s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 231s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 231s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 231s libnvme1 depends on libssl3 (>= 3.0.0). 231s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 231s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 231s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 231s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 231s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 231s kmod depends on libssl3 (>= 3.0.0). 231s dhcpcd-base depends on libssl3 (>= 3.0.0). 231s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 231s 231s (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 ... 75850 files and directories currently installed.) 231s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 231s Selecting previously unselected package libssl3t64:arm64. 232s (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 ... 75839 files and directories currently installed.) 232s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 232s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 232s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 232s Setting up openssl (3.0.13-0ubuntu1) ... 232s Processing triggers for man-db (2.12.0-3) ... 238s Processing triggers for libc-bin (2.39-0ubuntu2) ... 239s Reading package lists... 240s Building dependency tree... 240s Reading state information... 243s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 244s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 244s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 244s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 244s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 254s Reading package lists... 255s Reading package lists... 256s Building dependency tree... 256s Reading state information... 259s Calculating upgrade... 261s The following packages have been kept back: 261s curl 261s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 261s Reading package lists... 263s Building dependency tree... 263s Reading state information... 266s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 271s autopkgtest [17:19:05]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 272s autopkgtest [17:19:06]: @@@@@@@@@@@@@@@@@@@@ apt-source rna-star 276s Get:1 http://ftpmaster.internal/ubuntu noble/universe rna-star 2.7.11b+dfsg-1 (dsc) [2174 B] 276s Get:2 http://ftpmaster.internal/ubuntu noble/universe rna-star 2.7.11b+dfsg-1 (tar) [521 kB] 276s Get:3 http://ftpmaster.internal/ubuntu noble/universe rna-star 2.7.11b+dfsg-1 (diff) [379 kB] 277s gpgv: Signature made Fri Feb 9 16:25:56 2024 UTC 277s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 277s gpgv: Can't check signature: No public key 277s dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.11b+dfsg-1.dsc: no acceptable signature found 278s autopkgtest [17:19:12]: testing package rna-star version 2.7.11b+dfsg-1 278s autopkgtest [17:19:12]: build not needed 279s autopkgtest [17:19:13]: test command1: preparing testbed 282s Reading package lists... 283s Building dependency tree... 283s Reading state information... 284s Starting pkgProblemResolver with broken count: 0 285s Starting 2 pkgProblemResolver with broken count: 0 285s Done 288s The following additional packages will be installed: 288s libdeflate0 libgomp1 libhts3 libhtscodecs2 rna-star 288s The following NEW packages will be installed: 288s autopkgtest-satdep libdeflate0 libgomp1 libhts3 libhtscodecs2 rna-star 288s 0 upgraded, 6 newly installed, 0 to remove and 1 not upgraded. 288s Need to get 1478 kB/1479 kB of archives. 288s After this operation, 4441 kB of additional disk space will be used. 288s Get:1 /tmp/autopkgtest.E1h3xQ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 288s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 289s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 289s Get:4 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 289s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3 arm64 1.19+ds-1 [429 kB] 289s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 rna-star arm64 2.7.11b+dfsg-1 [784 kB] 292s Fetched 1478 kB in 1s (1447 kB/s) 292s Selecting previously unselected package libdeflate0:arm64. 292s (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 ... 75852 files and directories currently installed.) 292s Preparing to unpack .../0-libdeflate0_1.19-1_arm64.deb ... 292s Unpacking libdeflate0:arm64 (1.19-1) ... 292s Selecting previously unselected package libgomp1:arm64. 292s Preparing to unpack .../1-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 292s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 292s Selecting previously unselected package libhtscodecs2:arm64. 292s Preparing to unpack .../2-libhtscodecs2_1.6.0-1_arm64.deb ... 292s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 292s Selecting previously unselected package libhts3:arm64. 292s Preparing to unpack .../3-libhts3_1.19+ds-1_arm64.deb ... 292s Unpacking libhts3:arm64 (1.19+ds-1) ... 293s Selecting previously unselected package rna-star. 293s Preparing to unpack .../4-rna-star_2.7.11b+dfsg-1_arm64.deb ... 293s Unpacking rna-star (2.7.11b+dfsg-1) ... 293s Selecting previously unselected package autopkgtest-satdep. 293s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 293s Unpacking autopkgtest-satdep (0) ... 293s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 293s Setting up libdeflate0:arm64 (1.19-1) ... 293s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 293s Setting up libhts3:arm64 (1.19+ds-1) ... 293s Setting up rna-star (2.7.11b+dfsg-1) ... 293s Setting up autopkgtest-satdep (0) ... 293s Processing triggers for man-db (2.12.0-3) ... 295s Processing triggers for libc-bin (2.39-0ubuntu2) ... 305s (Reading database ... 75889 files and directories currently installed.) 305s Removing autopkgtest-satdep (0) ... 306s autopkgtest [17:19:40]: test command1: debian/tests/run_test.sh STAR 306s autopkgtest [17:19:40]: test command1: [----------------------- 307s STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /tmp/autopkgtest.E1h3xQ/build.PFY/src/debian/tests/foo.gtf 307s STAR version: 2.7.11b compiled: 2024-02-09T16:04:19+00:00 307s Mar 16 17:19:41 ..... started STAR run 307s Mar 16 17:19:41 ... starting to generate Genome files 307s Mar 16 17:19:41 ..... processing annotations GTF 307s !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 307s Mar 16 17:19:41 ... starting to sort Suffix Array. This may take a long time... 307s Mar 16 17:19:41 ... sorting Suffix Array chunks and saving them to disk... 307s Mar 16 17:19:41 ... loading chunks from disk, packing SA... 307s Mar 16 17:19:41 ... finished generating suffix array 307s Mar 16 17:19:41 ... generating Suffix Array index 307s Mar 16 17:19:41 ... completed Suffix Array index 307s Mar 16 17:19:41 ... writing Genome to disk ... 307s Mar 16 17:19:41 ... writing Suffix Array to disk ... 307s Mar 16 17:19:41 ... writing SAindex to disk 307s Mar 16 17:19:41 ..... finished successfully 307s STAR --runThreadN 1 --genomeDir . --readFilesIn reads.fastq 307s STAR version: 2.7.11b compiled: 2024-02-09T16:04:19+00:00 307s Mar 16 17:19:41 ..... started STAR run 307s Mar 16 17:19:41 ..... loading genome 307s Mar 16 17:19:41 ..... started mapping 308s Mar 16 17:19:42 ..... finished mapping 308s Mar 16 17:19:42 ..... finished successfully 309s autopkgtest [17:19:43]: test command1: -----------------------] 310s command1 PASS 310s autopkgtest [17:19:44]: test command1: - - - - - - - - - - results - - - - - - - - - - 311s autopkgtest [17:19:45]: @@@@@@@@@@@@@@@@@@@@ summary 311s command1 PASS 329s Creating nova instance adt-noble-arm64-rna-star-20240316-171434-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...