0s autopkgtest [22:59:21]: starting date: 2024-03-17 0s autopkgtest [22:59:21]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [22:59:21]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7g7b9m0z/out --timeout-copy=6000 --setup-commands 'ls /etc/apt/sources.list.d/*.list 2>/dev/null || true; 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,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:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade vcftools --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' -- lxd -r lxd-armhf-10.44.124.223 lxd-armhf-10.44.124.223:autopkgtest/ubuntu/noble/armhf 75s autopkgtest [23:00:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 78s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 79s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 79s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 80s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3726 kB] 80s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 80s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [574 kB] 80s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 80s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 80s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 80s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3500 kB] 80s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 80s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [33.8 kB] 80s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 92s Fetched 8505 kB in 4s (2025 kB/s) 93s Reading package lists... 108s /etc/apt/sources.list.d/proposed.list 110s tee: /proc/self/fd/2: Permission denied 143s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 143s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 143s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 143s Hit:4 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 143s Hit:5 http://ftpmaster.internal/ubuntu noble-security InRelease 143s Hit:6 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 144s Hit:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease 144s Hit:8 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 151s Reading package lists... 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 154s Calculating upgrade... 155s The following packages have been kept back: 155s curl openssl 155s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 158s 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. 160s autopkgtest [23:02:01]: rebooting testbed after setup commands that affected boot 195s autopkgtest [23:02:36]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 199s autopkgtest [23:02:40]: testbed dpkg architecture: armhf 216s autopkgtest [23:02:57]: @@@@@@@@@@@@@@@@@@@@ apt-source vcftools 225s Get:1 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (dsc) [2071 B] 225s Get:2 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (tar) [245 kB] 225s Get:3 http://ftpmaster.internal/ubuntu noble/universe vcftools 0.1.16-3 (diff) [14.0 kB] 225s gpgv: Signature made Thu Oct 7 06:07:18 2021 UTC 225s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 225s gpgv: issuer "tille@debian.org" 225s gpgv: Can't check signature: No public key 225s dpkg-source: warning: cannot verify inline signature for ./vcftools_0.1.16-3.dsc: no acceptable signature found 225s autopkgtest [23:03:06]: testing package vcftools version 0.1.16-3 225s autopkgtest [23:03:06]: build not needed 228s autopkgtest [23:03:09]: test run-unit-test: preparing testbed 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 245s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 246s Starting 2 pkgProblemResolver with broken count: 0 246s Done 246s Done 247s Starting pkgProblemResolver with broken count: 0 248s Starting 2 pkgProblemResolver with broken count: 0 248s Done 249s The following additional packages will be installed: 249s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 249s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 249s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 249s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 249s tabix vcftools 249s Recommended packages: 249s libalgorithm-diff-xs-perl 250s The following NEW packages will be installed: 250s libalgorithm-diff-perl libcapture-tiny-perl libclass-data-inheritable-perl 250s libdeflate0 libdevel-stacktrace-perl libexception-class-perl libhtscodecs2 250s libsub-uplevel-perl libtest-deep-perl libtest-differences-perl 250s libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl 250s tabix vcftools 250s 0 upgraded, 16 newly installed, 0 to remove and 2 not upgraded. 250s 1 not fully installed or removed. 250s Need to get 1231 kB of archives. 250s After this operation, 3854 kB of additional disk space will be used. 250s Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 250s Get:2 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB] 250s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf tabix armhf 1.19+ds-1.1build2 [428 kB] 250s Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libclass-data-inheritable-perl all 0.08-3 [8084 B] 250s Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 250s Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libexception-class-perl all 1.45-1 [28.6 kB] 250s Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libtest-deep-perl all 1.204-1 [47.1 kB] 250s Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libcapture-tiny-perl all 0.48-2 [20.2 kB] 251s Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libalgorithm-diff-perl all 1.201-1 [41.8 kB] 251s Get:10 http://ftpmaster.internal/ubuntu noble/universe armhf libtext-diff-perl all 1.45-2 [25.6 kB] 251s Get:11 http://ftpmaster.internal/ubuntu noble/universe armhf libtest-differences-perl all 0.71-1 [15.8 kB] 251s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf libsub-uplevel-perl all 0.2800-3 [11.6 kB] 251s Get:13 http://ftpmaster.internal/ubuntu noble/universe armhf libtest-exception-perl all 0.43-3 [13.4 kB] 251s Get:14 http://ftpmaster.internal/ubuntu noble/universe armhf libtest-warn-perl all 0.37-2 [12.6 kB] 251s Get:15 http://ftpmaster.internal/ubuntu noble/universe armhf libtest-most-perl all 0.38-1 [21.5 kB] 251s Get:16 http://ftpmaster.internal/ubuntu noble/universe armhf vcftools armhf 0.1.16-3 [428 kB] 252s Fetched 1231 kB in 1s (1388 kB/s) 252s Selecting previously unselected package libdeflate0:armhf. 252s (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 ... 58620 files and directories currently installed.) 252s Preparing to unpack .../00-libdeflate0_1.19-1_armhf.deb ... 252s Unpacking libdeflate0:armhf (1.19-1) ... 253s Selecting previously unselected package libhtscodecs2:armhf. 253s Preparing to unpack .../01-libhtscodecs2_1.6.0-1_armhf.deb ... 253s Unpacking libhtscodecs2:armhf (1.6.0-1) ... 253s Selecting previously unselected package tabix. 253s Preparing to unpack .../02-tabix_1.19+ds-1.1build2_armhf.deb ... 253s Unpacking tabix (1.19+ds-1.1build2) ... 253s Selecting previously unselected package libclass-data-inheritable-perl. 253s Preparing to unpack .../03-libclass-data-inheritable-perl_0.08-3_all.deb ... 253s Unpacking libclass-data-inheritable-perl (0.08-3) ... 253s Selecting previously unselected package libdevel-stacktrace-perl. 253s Preparing to unpack .../04-libdevel-stacktrace-perl_2.0500-1_all.deb ... 253s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 253s Selecting previously unselected package libexception-class-perl. 253s Preparing to unpack .../05-libexception-class-perl_1.45-1_all.deb ... 253s Unpacking libexception-class-perl (1.45-1) ... 254s Selecting previously unselected package libtest-deep-perl. 254s Preparing to unpack .../06-libtest-deep-perl_1.204-1_all.deb ... 254s Unpacking libtest-deep-perl (1.204-1) ... 254s Selecting previously unselected package libcapture-tiny-perl. 254s Preparing to unpack .../07-libcapture-tiny-perl_0.48-2_all.deb ... 254s Unpacking libcapture-tiny-perl (0.48-2) ... 254s Selecting previously unselected package libalgorithm-diff-perl. 254s Preparing to unpack .../08-libalgorithm-diff-perl_1.201-1_all.deb ... 254s Unpacking libalgorithm-diff-perl (1.201-1) ... 254s Selecting previously unselected package libtext-diff-perl. 254s Preparing to unpack .../09-libtext-diff-perl_1.45-2_all.deb ... 254s Unpacking libtext-diff-perl (1.45-2) ... 254s Selecting previously unselected package libtest-differences-perl. 254s Preparing to unpack .../10-libtest-differences-perl_0.71-1_all.deb ... 254s Unpacking libtest-differences-perl (0.71-1) ... 254s Selecting previously unselected package libsub-uplevel-perl. 254s Preparing to unpack .../11-libsub-uplevel-perl_0.2800-3_all.deb ... 254s Unpacking libsub-uplevel-perl (0.2800-3) ... 254s Selecting previously unselected package libtest-exception-perl. 254s Preparing to unpack .../12-libtest-exception-perl_0.43-3_all.deb ... 254s Unpacking libtest-exception-perl (0.43-3) ... 254s Selecting previously unselected package libtest-warn-perl. 254s Preparing to unpack .../13-libtest-warn-perl_0.37-2_all.deb ... 254s Unpacking libtest-warn-perl (0.37-2) ... 254s Selecting previously unselected package libtest-most-perl. 254s Preparing to unpack .../14-libtest-most-perl_0.38-1_all.deb ... 254s Unpacking libtest-most-perl (0.38-1) ... 254s Selecting previously unselected package vcftools. 254s Preparing to unpack .../15-vcftools_0.1.16-3_armhf.deb ... 254s Unpacking vcftools (0.1.16-3) ... 255s Setting up libhtscodecs2:armhf (1.6.0-1) ... 255s Setting up vcftools (0.1.16-3) ... 255s Setting up libtest-deep-perl (1.204-1) ... 255s Setting up libalgorithm-diff-perl (1.201-1) ... 255s Setting up libdeflate0:armhf (1.19-1) ... 255s Setting up libclass-data-inheritable-perl (0.08-3) ... 255s Setting up libtext-diff-perl (1.45-2) ... 255s Setting up libcapture-tiny-perl (0.48-2) ... 255s Setting up libsub-uplevel-perl (0.2800-3) ... 255s Setting up libdevel-stacktrace-perl (2.0500-1) ... 255s Setting up tabix (1.19+ds-1.1build2) ... 255s Setting up libtest-warn-perl (0.37-2) ... 255s Setting up libtest-differences-perl (0.71-1) ... 255s Setting up libexception-class-perl (1.45-1) ... 255s Setting up libtest-exception-perl (0.43-3) ... 255s Setting up libtest-most-perl (0.38-1) ... 255s Setting up autopkgtest-satdep (0) ... 255s Processing triggers for man-db (2.12.0-3) ... 258s Processing triggers for libc-bin (2.39-0ubuntu2) ... 276s (Reading database ... 58900 files and directories currently installed.) 276s Removing autopkgtest-satdep (0) ... 287s autopkgtest [23:04:08]: test run-unit-test: [----------------------- 289s FaSlice.pm 289s Vcf.pm 289s VcfStats.pm 289s fill-aa 289s fill-an-ac 289s fill-fs 289s fill-ref-md5 289s test.t 289s vcf-annotate 289s vcf-compare 289s vcf-concat 289s vcf-consensus 289s vcf-contrast 289s vcf-convert 289s vcf-fix-newlines 289s vcf-fix-ploidy 289s vcf-indel-stats 289s vcf-isec 289s vcf-merge 289s vcf-phased-join 289s vcf-query 289s vcf-shuffle-cols 289s vcf-sort 289s vcf-stats 289s vcf-subset 289s vcf-to-tab 289s vcf-tstv 289s vcf-validator 289s vcftools 290s 1..68 290s ok 1 - Is bgzip OK? .. cat /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf | bgzip -c > /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 290s ok 2 - Is tabix OK? .. tabix /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/merge-test-a.vcf.gz 290s ok 3 - Testing validator .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/valid-3.3.vcf 290s ok 4 - Testing validator .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/valid-4.0.vcf 291s ok 5 - Testing validator .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/valid-4.1.vcf 291s ok 6 - Testing validator .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate /tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite/../testdata/floats.vcf 291s ok 7 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 291s ok 8 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 291s ok 9 - Testing formatting followed by validation .. perl -I/tmp/autopkgtest.n2vDZ5/autopkgtest_tmp/testsuite -MVcf -e validate 2>&1 291s ok 10 - Testing next_data_array 291s ok 11 - Testing next_data_array 291s ok 12 - Testing next_data_array 291s ok 13 - Testing next_data_array 291s ok 14 - Testing add_columns with genotypes full, 4.0. 291s ok 15 - Testing add_columns with genotypes brief, 4.0. 291s ok 16 - Testing add_columns brief, 4.0. 291s ok 17 - Testing add_columns no gtypes, 4.0. 292s ok 18 - Testing vcf-isec .. perl -I../. -MVcf /usr/bin/vcf-isec -f -n +2 merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz 292s ok 19 - Testing vcf-query .. perl -I../. -MVcf /usr/bin/vcf-query -f '%CHROM:%POS\tref=%REF\talt=%ALT\tqual=%QUAL\t%INFO/DP[\t%SAMPLE=%GT]\n' cmp-test-a.vcf 292s ok 20 - Testing vcf-shuffle-cols .. perl -I../. -MVcf /usr/bin/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf 293s ok 21 - Testing vcf-concat .. perl -I../. -MVcf /usr/bin/vcf-concat -s 3 concat-a.vcf.gz concat-b.vcf.gz concat-c.vcf.gz 293s ok 22 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/fill-an-ac concat-a.vcf 293s ok 23 - Testing fill-an-ac .. perl -I../. -MVcf /usr/bin/vcf-indel-stats -e indel-stats.tab < indel-stats.vcf 294s Looks as fasta file snippet, the sequence 1 starts at position 1 294s Looks as fasta file snippet, the sequence 2 starts at position 1 294s ok 24 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus consensus.vcf.gz < consensus.fa 294s Looks as fasta file snippet, the sequence 1 starts at position 1 294s Looks as fasta file snippet, the sequence 2 starts at position 1 294s ok 25 - Testing vcf-consensus .. perl -I../. -MVcf /usr/bin/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa 294s ok 26 - Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../. -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n' 294s ok 27 - Testing API event_type(A,C) .. s 1 C 294s ok 28 - Testing API event_type(A,ACGT) .. i 3 CGT 294s ok 29 - Testing API event_type(ACGT,A) .. i -3 CGT 294s ok 30 - Testing API event_type(ACGT,ACT) .. i -1 G 294s ok 31 - Testing API event_type(ACGT,AAA) .. o 3 AAA 294s ok 32 - Testing API event_type(A,.) .. r 0 A 294s ok 33 - Testing API event_type(A,) .. u 0 294s ok 34 - Testing API event_type(ACG,AGC) .. s 2 AGC 294s ok 35 - Testing API event_type(A,.A) .. b 294s ok 36 - Testing API event_type(A,A.) .. b 294s ok 37 - Testing get_tag_index(GT:GL:PL,'GT',':') 294s ok 38 - Testing get_tag_index(GT:GL:PL,'GL',':') 294s ok 39 - Testing get_tag_index(GT:GL:PL,'PL',':') 294s ok 40 - Testing get_tag_index(GT:GL:PL,0,':') 294s ok 41 - Testing get_tag_index(GT:GL:PL,1,':') 294s ok 42 - Testing get_tag_index(GT:GL:PL,2,':') 294s ok 43 - Testing get_tag_index(GT:GL:PL,'XX',0,':') 294s ok 44 - Testing get_tag_index(GT:GL:PL,'XX',1,':') 294s ok 45 - Testing get_tag_index(GT:GL:PL,'XX',2,':') 294s ok 46 - Testing get_tag_index(GT:GL:PL,'XX',4,':') 294s ok 47 - Testing decode_genotype('C',['G','T'],'0/1/2|1/0|1|2') 294s ok 48 - Testing decode_genotype('C',['G','T'],'2|1') 294s ok 49 - Testing decode_genotype('C',['G','T'],'2') 294s ok 50 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'NS') 294s ok 51 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AF') 294s ok 52 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'AFA') 294s ok 53 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'HM') 294s ok 54 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DB') 294s ok 55 - Testing get_info_field(NS=2;HM;AF=0.333;AFA=T;DB,'DBX') 294s ok 56 - Testing get_info_field('DB','DB') 294s ok 57 - Testing get_info_field('XDB','DB') 294s ok 58 - Testing split_gt('0/1') 294s ok 59 - Testing split_gt('0') 294s ok 60 - Testing normalize_alleles(TTGGTAT,TTGGTATCTAGTGGTAT,TGGTATCTAGTGGTAT) 294s ok 61 - Testing normalize_alleles(TT,TCTAGTGGTAAT,TCT) 294s ok 62 - Testing normalize_alleles(TGGGGGG,TGGGGGGG) 294s ok 63 - Testing normalize_alleles(CAAAAAA,CAAAAA) 294s ok 64 - Testing normalize_alleles(CA,CT) 294s ok 65 - Testing normalize_alleles_pos(GAACCCACA,GA) 294s ok 66 - Testing normalize_alleles_pos(CAGTAAAA,CAGAAAA) 294s ok 67 - Testing normalize_alleles_pos(CAGTAAA,CAGAAAA) 294s ok 68 - Testing normalize_alleles_pos(GA,GACC) 294s PASS 295s autopkgtest [23:04:16]: test run-unit-test: -----------------------] 299s autopkgtest [23:04:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 299s run-unit-test PASS 303s autopkgtest [23:04:24]: @@@@@@@@@@@@@@@@@@@@ summary 303s run-unit-test PASS