0s autopkgtest [12:41:56]: starting date and time: 2024-11-04 12:41:56+0000 0s autopkgtest [12:41:56]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [12:41:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ofkotzw3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade libbio-db-hts-perl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-38.secgroup --name adt-plucky-amd64-libbio-db-hts-perl-20241104-124156-juju-7f2275-prod-proposed-migration-environment-2-8b0bee51-dd16-47a2-9247-23f6907eb5c2 --image adt/ubuntu-plucky-amd64-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,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/ 57s autopkgtest [12:42:53]: testbed dpkg architecture: amd64 57s autopkgtest [12:42:53]: testbed apt version: 2.9.8 57s autopkgtest [12:42:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 58s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 58s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 58s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 58s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 58s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 58s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 58s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 58s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 58s Fetched 5618 kB in 1s (9202 kB/s) 58s Reading package lists... 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 61s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 61s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 62s Reading package lists... 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s autopkgtest [12:43:01]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 65s autopkgtest [12:43:01]: @@@@@@@@@@@@@@@@@@@@ apt-source libbio-db-hts-perl 66s Get:1 http://ftpmaster.internal/ubuntu plucky/universe libbio-db-hts-perl 3.01-4build4 (dsc) [2270 B] 66s Get:2 http://ftpmaster.internal/ubuntu plucky/universe libbio-db-hts-perl 3.01-4build4 (tar) [5251 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky/universe libbio-db-hts-perl 3.01-4build4 (diff) [4060 B] 66s gpgv: Signature made Sun Oct 20 08:30:39 2024 UTC 66s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 66s gpgv: Can't check signature: No public key 66s dpkg-source: warning: cannot verify inline signature for ./libbio-db-hts-perl_3.01-4build4.dsc: no acceptable signature found 66s autopkgtest [12:43:02]: testing package libbio-db-hts-perl version 3.01-4build4 67s autopkgtest [12:43:03]: build not needed 68s autopkgtest [12:43:04]: test autodep8-perl-build-deps: preparing testbed 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 69s Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 69s The following additional packages will be installed: 69s autoconf autodep8 automake autopoint autotools-dev build-essential cpp 69s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu dctrl-tools debhelper 69s debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-14 69s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 69s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 69s libarchive-zip-perl libasan8 libbio-db-hts-perl libbio-perl-perl 69s libbrotli-dev libbz2-dev libcc1-0 libcurl4-gnutls-dev libdata-stag-perl 69s libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 69s libextutils-pkgconfig-perl libfile-stripnondeterminism-perl libgcc-14-dev 69s libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 69s libgnutls28-dev libgomp1 libhts-dev libhts3t64 libhtscodecs2 libhwasan0 69s libidn2-dev libio-string-perl libisl23 libitm1 liblsan0 liblzma-dev 69s libmodule-build-perl libmpc3 libnghttp2-dev libp11-kit-dev libpkgconf3 69s libpsl-dev libquadmath0 librtmp-dev libssh2-1-dev libssl-dev 69s libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 69s libzstd-dev m4 nettle-dev pkg-config pkg-perl-autopkgtest pkgconf 69s pkgconf-bin po-debconf zlib1g-dev 69s Suggested packages: 69s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 69s cpp-14-doc debtags dh-make g++-multilib g++-14-multilib gcc-14-doc 69s gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-14-multilib 69s gdb-x86-64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev bioperl 69s libxml-sax-expatxs-perl libcurl4-doc libidn-dev libkrb5-dev libldap2-dev 69s gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc 69s liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc 69s libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl 69s Recommended packages: 69s bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl 69s libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl 69s libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl 69s libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl 69s libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl 69s libset-scalar-perl libsoap-lite-perl libsort-naturally-perl 69s libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl 69s libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl 69s libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl 69s libxml-writer-perl libxml-libxml-perl libwww-perl bzip2-doc perl-tk 69s libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl 69s libxml-perl libarchive-cpio-perl libmodule-signature-perl libpod-readme-perl 69s libsoftware-license-perl libtasn1-doc libltdl-dev libmail-sendmail-perl 69s The following NEW packages will be installed: 69s autoconf autodep8 automake autopkgtest-satdep autopoint autotools-dev 69s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 69s dctrl-tools debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz 69s g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 69s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 69s libarchive-zip-perl libasan8 libbio-db-hts-perl libbio-perl-perl 69s libbrotli-dev libbz2-dev libcc1-0 libcurl4-gnutls-dev libdata-stag-perl 69s libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64 69s libextutils-pkgconfig-perl libfile-stripnondeterminism-perl libgcc-14-dev 69s libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 69s libgnutls28-dev libgomp1 libhts-dev libhts3t64 libhtscodecs2 libhwasan0 69s libidn2-dev libio-string-perl libisl23 libitm1 liblsan0 liblzma-dev 69s libmodule-build-perl libmpc3 libnghttp2-dev libp11-kit-dev libpkgconf3 69s libpsl-dev libquadmath0 librtmp-dev libssh2-1-dev libssl-dev 69s libstdc++-14-dev libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 69s libzstd-dev m4 nettle-dev pkg-config pkg-perl-autopkgtest pkgconf 69s pkgconf-bin po-debconf zlib1g-dev 69s 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 89.5 MB/89.5 MB of archives. 69s After this operation, 298 MB of additional disk space will be used. 69s Get:1 /tmp/autopkgtest.efi4EO/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [800 B] 69s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 69s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 69s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autodep8 all 0.28+nmu1ubuntu1 [13.7 kB] 69s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 69s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 69s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 69s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 69s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 69s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [11.9 MB] 70s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-7ubuntu1 [1026 B] 70s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 70s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 70s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-7ubuntu1 [47.6 kB] 70s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 70s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-7ubuntu1 [29.1 kB] 70s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-7ubuntu1 [2998 kB] 70s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-7ubuntu1 [1316 kB] 70s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-7ubuntu1 [2733 kB] 70s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-7ubuntu1 [1177 kB] 70s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-7ubuntu1 [1634 kB] 70s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-7ubuntu1 [153 kB] 70s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-7ubuntu1 [2814 kB] 70s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [23.4 MB] 70s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-7ubuntu1 [526 kB] 70s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 70s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 70s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-7ubuntu1 [2503 kB] 70s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [13.4 MB] 70s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-7ubuntu1 [19.8 kB] 70s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 70s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 70s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 70s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 70s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 70s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 70s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 70s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 70s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 70s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 70s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 70s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 70s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 70s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 70s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 70s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 70s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 70s Get:49 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 70s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 70s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdata-stag-perl all 0.14-3 [372 kB] 70s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbio-perl-perl all 1.7.8-1 [2580 kB] 70s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbio-db-hts-perl amd64 3.01-4build4 [141 kB] 70s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli-dev amd64 1.1.0-2build2 [353 kB] 70s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 70s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [144 kB] 70s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libunbound8 amd64 1.20.0-1ubuntu2.1 [447 kB] 70s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-dane0t64 amd64 3.8.6-2ubuntu1 [24.0 kB] 70s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2ubuntu1 [24.2 kB] 70s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn2-dev amd64 2.3.7-2build2 [120 kB] 70s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit-dev amd64 0.25.5-2ubuntu1 [22.7 kB] 70s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6-dev amd64 4.19.0-3build1 [90.5 kB] 70s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2ubuntu7 [10.0 kB] 70s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2ubuntu7 [341 kB] 70s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 nettle-dev amd64 3.10-1 [1172 kB] 70s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls28-dev amd64 3.8.6-2ubuntu1 [1069 kB] 70s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-3ubuntu1 [31.0 kB] 70s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-3ubuntu1 [21.2 kB] 70s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-3ubuntu1 [16.8 kB] 70s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libnghttp2-dev amd64 1.62.1-2 [118 kB] 70s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libpsl-dev amd64 0.21.2-1.1build1 [76.4 kB] 70s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 70s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2build7 [66.7 kB] 70s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl-dev amd64 3.3.1-2ubuntu2 [2686 kB] 70s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libssh2-1-dev amd64 1.11.0-7 [260 kB] 70s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [371 kB] 70s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4-gnutls-dev amd64 8.9.1-2ubuntu2 [476 kB] 70s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.21-1 [56.9 kB] 70s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pkg-config amd64 1.8.1-3ubuntu1 [7402 B] 70s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libextutils-pkgconfig-perl all 1.16-3 [8524 B] 70s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.2-2 [176 kB] 70s Get:82 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts-dev amd64 1.20+ds-2 [6298 kB] 70s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmodule-build-perl all 0.423400-2 [200 kB] 70s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-perl-autopkgtest all 0.79 [18.5 kB] 71s Fetched 89.5 MB in 1s (103 MB/s) 71s Selecting previously unselected package m4. 71s (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 ... 75323 files and directories currently installed.) 71s Preparing to unpack .../00-m4_1.4.19-4build1_amd64.deb ... 71s Unpacking m4 (1.4.19-4build1) ... 71s Selecting previously unselected package autoconf. 71s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 71s Unpacking autoconf (2.72-3) ... 71s Selecting previously unselected package dctrl-tools. 71s Preparing to unpack .../02-dctrl-tools_2.24-3build3_amd64.deb ... 71s Unpacking dctrl-tools (2.24-3build3) ... 71s Selecting previously unselected package autodep8. 71s Preparing to unpack .../03-autodep8_0.28+nmu1ubuntu1_all.deb ... 71s Unpacking autodep8 (0.28+nmu1ubuntu1) ... 71s Selecting previously unselected package autotools-dev. 71s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 71s Unpacking autotools-dev (20220109.1) ... 71s Selecting previously unselected package automake. 71s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 71s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 71s Selecting previously unselected package autopoint. 71s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 71s Unpacking autopoint (0.22.5-2) ... 71s Selecting previously unselected package libisl23:amd64. 71s Preparing to unpack .../07-libisl23_0.27-1_amd64.deb ... 71s Unpacking libisl23:amd64 (0.27-1) ... 71s Selecting previously unselected package libmpc3:amd64. 71s Preparing to unpack .../08-libmpc3_1.3.1-1build2_amd64.deb ... 71s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 71s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 71s Preparing to unpack .../09-cpp-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 71s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 71s Selecting previously unselected package cpp-14. 71s Preparing to unpack .../10-cpp-14_14.2.0-7ubuntu1_amd64.deb ... 71s Unpacking cpp-14 (14.2.0-7ubuntu1) ... 71s Selecting previously unselected package cpp-x86-64-linux-gnu. 71s Preparing to unpack .../11-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 71s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 71s Selecting previously unselected package cpp. 71s Preparing to unpack .../12-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 71s Unpacking cpp (4:14.1.0-2ubuntu1) ... 71s Selecting previously unselected package libcc1-0:amd64. 71s Preparing to unpack .../13-libcc1-0_14.2.0-7ubuntu1_amd64.deb ... 71s Unpacking libcc1-0:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libgomp1:amd64. 72s Preparing to unpack .../14-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libitm1:amd64. 72s Preparing to unpack .../15-libitm1_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libitm1:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libasan8:amd64. 72s Preparing to unpack .../16-libasan8_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libasan8:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package liblsan0:amd64. 72s Preparing to unpack .../17-liblsan0_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking liblsan0:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libtsan2:amd64. 72s Preparing to unpack .../18-libtsan2_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libtsan2:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libubsan1:amd64. 72s Preparing to unpack .../19-libubsan1_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libubsan1:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libhwasan0:amd64. 72s Preparing to unpack .../20-libhwasan0_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libhwasan0:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libquadmath0:amd64. 72s Preparing to unpack .../21-libquadmath0_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libquadmath0:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package libgcc-14-dev:amd64. 72s Preparing to unpack .../22-libgcc-14-dev_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 72s Preparing to unpack .../23-gcc-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 72s Selecting previously unselected package gcc-14. 72s Preparing to unpack .../24-gcc-14_14.2.0-7ubuntu1_amd64.deb ... 72s Unpacking gcc-14 (14.2.0-7ubuntu1) ... 73s Selecting previously unselected package gcc-x86-64-linux-gnu. 73s Preparing to unpack .../25-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 73s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 73s Selecting previously unselected package gcc. 73s Preparing to unpack .../26-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 73s Unpacking gcc (4:14.1.0-2ubuntu1) ... 73s Selecting previously unselected package libstdc++-14-dev:amd64. 73s Preparing to unpack .../27-libstdc++-14-dev_14.2.0-7ubuntu1_amd64.deb ... 73s Unpacking libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ... 73s Selecting previously unselected package g++-14-x86-64-linux-gnu. 73s Preparing to unpack .../28-g++-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 73s Unpacking g++-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 73s Selecting previously unselected package g++-14. 73s Preparing to unpack .../29-g++-14_14.2.0-7ubuntu1_amd64.deb ... 73s Unpacking g++-14 (14.2.0-7ubuntu1) ... 73s Selecting previously unselected package g++-x86-64-linux-gnu. 73s Preparing to unpack .../30-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 73s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 73s Selecting previously unselected package g++. 73s Preparing to unpack .../31-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 73s Unpacking g++ (4:14.1.0-2ubuntu1) ... 73s Selecting previously unselected package build-essential. 73s Preparing to unpack .../32-build-essential_12.10ubuntu1_amd64.deb ... 73s Unpacking build-essential (12.10ubuntu1) ... 73s Selecting previously unselected package libdebhelper-perl. 73s Preparing to unpack .../33-libdebhelper-perl_13.20ubuntu1_all.deb ... 73s Unpacking libdebhelper-perl (13.20ubuntu1) ... 73s Selecting previously unselected package libtool. 73s Preparing to unpack .../34-libtool_2.4.7-7build1_all.deb ... 73s Unpacking libtool (2.4.7-7build1) ... 73s Selecting previously unselected package dh-autoreconf. 73s Preparing to unpack .../35-dh-autoreconf_20_all.deb ... 73s Unpacking dh-autoreconf (20) ... 73s Selecting previously unselected package libarchive-zip-perl. 73s Preparing to unpack .../36-libarchive-zip-perl_1.68-1_all.deb ... 73s Unpacking libarchive-zip-perl (1.68-1) ... 73s Selecting previously unselected package libfile-stripnondeterminism-perl. 73s Preparing to unpack .../37-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 73s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 73s Selecting previously unselected package dh-strip-nondeterminism. 73s Preparing to unpack .../38-dh-strip-nondeterminism_1.14.0-1_all.deb ... 73s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 73s Selecting previously unselected package debugedit. 73s Preparing to unpack .../39-debugedit_1%3a5.1-1_amd64.deb ... 73s Unpacking debugedit (1:5.1-1) ... 73s Selecting previously unselected package dwz. 73s Preparing to unpack .../40-dwz_0.15-1build6_amd64.deb ... 73s Unpacking dwz (0.15-1build6) ... 73s Selecting previously unselected package gettext. 73s Preparing to unpack .../41-gettext_0.22.5-2_amd64.deb ... 73s Unpacking gettext (0.22.5-2) ... 73s Selecting previously unselected package intltool-debian. 73s Preparing to unpack .../42-intltool-debian_0.35.0+20060710.6_all.deb ... 73s Unpacking intltool-debian (0.35.0+20060710.6) ... 73s Selecting previously unselected package po-debconf. 73s Preparing to unpack .../43-po-debconf_1.0.21+nmu1_all.deb ... 73s Unpacking po-debconf (1.0.21+nmu1) ... 74s Selecting previously unselected package debhelper. 74s Preparing to unpack .../44-debhelper_13.20ubuntu1_all.deb ... 74s Unpacking debhelper (13.20ubuntu1) ... 74s Selecting previously unselected package libdeflate0:amd64. 74s Preparing to unpack .../45-libdeflate0_1.21-1_amd64.deb ... 74s Unpacking libdeflate0:amd64 (1.21-1) ... 74s Selecting previously unselected package libhtscodecs2:amd64. 74s Preparing to unpack .../46-libhtscodecs2_1.6.0-1build1_amd64.deb ... 74s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 74s Selecting previously unselected package libhts3t64:amd64. 74s Preparing to unpack .../47-libhts3t64_1.20+ds-2_amd64.deb ... 74s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 74s Selecting previously unselected package libio-string-perl. 74s Preparing to unpack .../48-libio-string-perl_1.08-4_all.deb ... 74s Unpacking libio-string-perl (1.08-4) ... 74s Selecting previously unselected package libdata-stag-perl. 74s Preparing to unpack .../49-libdata-stag-perl_0.14-3_all.deb ... 74s Unpacking libdata-stag-perl (0.14-3) ... 74s Selecting previously unselected package libbio-perl-perl. 74s Preparing to unpack .../50-libbio-perl-perl_1.7.8-1_all.deb ... 74s Unpacking libbio-perl-perl (1.7.8-1) ... 74s Selecting previously unselected package libbio-db-hts-perl. 74s Preparing to unpack .../51-libbio-db-hts-perl_3.01-4build4_amd64.deb ... 74s Unpacking libbio-db-hts-perl (3.01-4build4) ... 74s Selecting previously unselected package libbrotli-dev:amd64. 74s Preparing to unpack .../52-libbrotli-dev_1.1.0-2build2_amd64.deb ... 74s Unpacking libbrotli-dev:amd64 (1.1.0-2build2) ... 74s Selecting previously unselected package libbz2-dev:amd64. 74s Preparing to unpack .../53-libbz2-dev_1.0.8-6_amd64.deb ... 74s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 74s Selecting previously unselected package libevent-2.1-7t64:amd64. 74s Preparing to unpack .../54-libevent-2.1-7t64_2.1.12-stable-10_amd64.deb ... 74s Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... 74s Selecting previously unselected package libunbound8:amd64. 74s Preparing to unpack .../55-libunbound8_1.20.0-1ubuntu2.1_amd64.deb ... 74s Unpacking libunbound8:amd64 (1.20.0-1ubuntu2.1) ... 74s Selecting previously unselected package libgnutls-dane0t64:amd64. 74s Preparing to unpack .../56-libgnutls-dane0t64_3.8.6-2ubuntu1_amd64.deb ... 74s Unpacking libgnutls-dane0t64:amd64 (3.8.6-2ubuntu1) ... 74s Selecting previously unselected package libgnutls-openssl27t64:amd64. 74s Preparing to unpack .../57-libgnutls-openssl27t64_3.8.6-2ubuntu1_amd64.deb ... 74s Unpacking libgnutls-openssl27t64:amd64 (3.8.6-2ubuntu1) ... 74s Selecting previously unselected package libidn2-dev:amd64. 74s Preparing to unpack .../58-libidn2-dev_2.3.7-2build2_amd64.deb ... 74s Unpacking libidn2-dev:amd64 (2.3.7-2build2) ... 74s Selecting previously unselected package libp11-kit-dev:amd64. 74s Preparing to unpack .../59-libp11-kit-dev_0.25.5-2ubuntu1_amd64.deb ... 74s Unpacking libp11-kit-dev:amd64 (0.25.5-2ubuntu1) ... 74s Selecting previously unselected package libtasn1-6-dev:amd64. 74s Preparing to unpack .../60-libtasn1-6-dev_4.19.0-3build1_amd64.deb ... 74s Unpacking libtasn1-6-dev:amd64 (4.19.0-3build1) ... 74s Selecting previously unselected package libgmpxx4ldbl:amd64. 74s Preparing to unpack .../61-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_amd64.deb ... 74s Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 74s Selecting previously unselected package libgmp-dev:amd64. 74s Preparing to unpack .../62-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_amd64.deb ... 74s Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 74s Selecting previously unselected package nettle-dev:amd64. 74s Preparing to unpack .../63-nettle-dev_3.10-1_amd64.deb ... 74s Unpacking nettle-dev:amd64 (3.10-1) ... 74s Selecting previously unselected package libgnutls28-dev:amd64. 74s Preparing to unpack .../64-libgnutls28-dev_3.8.6-2ubuntu1_amd64.deb ... 74s Unpacking libgnutls28-dev:amd64 (3.8.6-2ubuntu1) ... 74s Selecting previously unselected package libpkgconf3:amd64. 74s Preparing to unpack .../65-libpkgconf3_1.8.1-3ubuntu1_amd64.deb ... 74s Unpacking libpkgconf3:amd64 (1.8.1-3ubuntu1) ... 74s Selecting previously unselected package pkgconf-bin. 74s Preparing to unpack .../66-pkgconf-bin_1.8.1-3ubuntu1_amd64.deb ... 74s Unpacking pkgconf-bin (1.8.1-3ubuntu1) ... 74s Selecting previously unselected package pkgconf:amd64. 74s Preparing to unpack .../67-pkgconf_1.8.1-3ubuntu1_amd64.deb ... 74s Unpacking pkgconf:amd64 (1.8.1-3ubuntu1) ... 75s Selecting previously unselected package libnghttp2-dev:amd64. 75s Preparing to unpack .../68-libnghttp2-dev_1.62.1-2_amd64.deb ... 75s Unpacking libnghttp2-dev:amd64 (1.62.1-2) ... 75s Selecting previously unselected package libpsl-dev:amd64. 75s Preparing to unpack .../69-libpsl-dev_0.21.2-1.1build1_amd64.deb ... 75s Unpacking libpsl-dev:amd64 (0.21.2-1.1build1) ... 75s Selecting previously unselected package zlib1g-dev:amd64. 75s Preparing to unpack .../70-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 75s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 75s Selecting previously unselected package librtmp-dev:amd64. 75s Preparing to unpack .../71-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_amd64.deb ... 75s Unpacking librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2build7) ... 75s Selecting previously unselected package libssl-dev:amd64. 75s Preparing to unpack .../72-libssl-dev_3.3.1-2ubuntu2_amd64.deb ... 75s Unpacking libssl-dev:amd64 (3.3.1-2ubuntu2) ... 75s Selecting previously unselected package libssh2-1-dev:amd64. 75s Preparing to unpack .../73-libssh2-1-dev_1.11.0-7_amd64.deb ... 75s Unpacking libssh2-1-dev:amd64 (1.11.0-7) ... 75s Selecting previously unselected package libzstd-dev:amd64. 75s Preparing to unpack .../74-libzstd-dev_1.5.6+dfsg-1_amd64.deb ... 75s Unpacking libzstd-dev:amd64 (1.5.6+dfsg-1) ... 75s Selecting previously unselected package libcurl4-gnutls-dev:amd64. 75s Preparing to unpack .../75-libcurl4-gnutls-dev_8.9.1-2ubuntu2_amd64.deb ... 75s Unpacking libcurl4-gnutls-dev:amd64 (8.9.1-2ubuntu2) ... 75s Selecting previously unselected package libdeflate-dev:amd64. 75s Preparing to unpack .../76-libdeflate-dev_1.21-1_amd64.deb ... 75s Unpacking libdeflate-dev:amd64 (1.21-1) ... 75s Selecting previously unselected package pkg-config:amd64. 75s Preparing to unpack .../77-pkg-config_1.8.1-3ubuntu1_amd64.deb ... 75s Unpacking pkg-config:amd64 (1.8.1-3ubuntu1) ... 75s Selecting previously unselected package libextutils-pkgconfig-perl. 75s Preparing to unpack .../78-libextutils-pkgconfig-perl_1.16-3_all.deb ... 75s Unpacking libextutils-pkgconfig-perl (1.16-3) ... 75s Selecting previously unselected package liblzma-dev:amd64. 75s Preparing to unpack .../79-liblzma-dev_5.6.2-2_amd64.deb ... 75s Unpacking liblzma-dev:amd64 (5.6.2-2) ... 75s Selecting previously unselected package libhts-dev:amd64. 75s Preparing to unpack .../80-libhts-dev_1.20+ds-2_amd64.deb ... 75s Unpacking libhts-dev:amd64 (1.20+ds-2) ... 75s Selecting previously unselected package libmodule-build-perl. 75s Preparing to unpack .../81-libmodule-build-perl_0.423400-2_all.deb ... 75s Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' 75s Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' 75s Unpacking libmodule-build-perl (0.423400-2) ... 75s Selecting previously unselected package pkg-perl-autopkgtest. 75s Preparing to unpack .../82-pkg-perl-autopkgtest_0.79_all.deb ... 75s Unpacking pkg-perl-autopkgtest (0.79) ... 75s Selecting previously unselected package autopkgtest-satdep. 75s Preparing to unpack .../83-1-autopkgtest-satdep.deb ... 75s Unpacking autopkgtest-satdep (0) ... 75s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 75s Setting up libgnutls-openssl27t64:amd64 (3.8.6-2ubuntu1) ... 75s Setting up libzstd-dev:amd64 (1.5.6+dfsg-1) ... 75s Setting up libarchive-zip-perl (1.68-1) ... 75s Setting up libdebhelper-perl (13.20ubuntu1) ... 75s Setting up libdeflate0:amd64 (1.21-1) ... 75s Setting up m4 (1.4.19-4build1) ... 75s Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... 75s Setting up libgomp1:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libpsl-dev:amd64 (0.21.2-1.1build1) ... 75s Setting up libmodule-build-perl (0.423400-2) ... 75s Setting up libio-string-perl (1.08-4) ... 75s Setting up autotools-dev (20220109.1) ... 75s Setting up libunbound8:amd64 (1.20.0-1ubuntu2.1) ... 75s Setting up libpkgconf3:amd64 (1.8.1-3ubuntu1) ... 75s Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 75s Setting up libgnutls-dane0t64:amd64 (3.8.6-2ubuntu1) ... 75s Setting up libquadmath0:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libssl-dev:amd64 (3.3.1-2ubuntu2) ... 75s Setting up libmpc3:amd64 (1.3.1-1build2) ... 75s Setting up autopoint (0.22.5-2) ... 75s Setting up pkgconf-bin (1.8.1-3ubuntu1) ... 75s Setting up libidn2-dev:amd64 (2.3.7-2build2) ... 75s Setting up autoconf (2.72-3) ... 75s Setting up liblzma-dev:amd64 (5.6.2-2) ... 75s Setting up libubsan1:amd64 (14.2.0-7ubuntu1) ... 75s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 75s Setting up dwz (0.15-1build6) ... 75s Setting up libdata-stag-perl (0.14-3) ... 75s Setting up libhwasan0:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libasan8:amd64 (14.2.0-7ubuntu1) ... 75s Setting up debugedit (1:5.1-1) ... 75s Setting up libhts3t64:amd64 (1.20+ds-2) ... 75s Setting up libbio-perl-perl (1.7.8-1) ... 75s Setting up libtsan2:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libisl23:amd64 (0.27-1) ... 75s Setting up libtasn1-6-dev:amd64 (4.19.0-3build1) ... 75s Setting up libdeflate-dev:amd64 (1.21-1) ... 75s Setting up libcc1-0:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libbrotli-dev:amd64 (1.1.0-2build2) ... 75s Setting up liblsan0:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libp11-kit-dev:amd64 (0.25.5-2ubuntu1) ... 75s Setting up dctrl-tools (2.24-3build3) ... 75s Setting up libitm1:amd64 (14.2.0-7ubuntu1) ... 75s Setting up autodep8 (0.28+nmu1ubuntu1) ... 75s Setting up libbz2-dev:amd64 (1.0.8-6) ... 75s Setting up automake (1:1.16.5-1.3ubuntu1) ... 75s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 75s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 75s Setting up gettext (0.22.5-2) ... 75s Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2ubuntu7) ... 75s Setting up nettle-dev:amd64 (3.10-1) ... 75s Setting up libbio-db-hts-perl (3.01-4build4) ... 75s Setting up pkgconf:amd64 (1.8.1-3ubuntu1) ... 75s Setting up intltool-debian (0.35.0+20060710.6) ... 75s Setting up pkg-config:amd64 (1.8.1-3ubuntu1) ... 75s Setting up cpp-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 75s Setting up libssh2-1-dev:amd64 (1.11.0-7) ... 75s Setting up pkg-perl-autopkgtest (0.79) ... 75s Setting up cpp-14 (14.2.0-7ubuntu1) ... 75s Setting up dh-strip-nondeterminism (1.14.0-1) ... 75s Setting up libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ... 75s Setting up libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ... 75s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 75s Setting up libgnutls28-dev:amd64 (3.8.6-2ubuntu1) ... 75s Setting up libnghttp2-dev:amd64 (1.62.1-2) ... 75s Setting up libextutils-pkgconfig-perl (1.16-3) ... 75s Setting up po-debconf (1.0.21+nmu1) ... 75s Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2build7) ... 75s Setting up cpp (4:14.1.0-2ubuntu1) ... 75s Setting up gcc-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 75s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 75s Setting up libcurl4-gnutls-dev:amd64 (8.9.1-2ubuntu2) ... 75s Setting up gcc-14 (14.2.0-7ubuntu1) ... 75s Setting up g++-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 75s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 75s Setting up g++-14 (14.2.0-7ubuntu1) ... 75s Setting up libtool (2.4.7-7build1) ... 75s Setting up libhts-dev:amd64 (1.20+ds-2) ... 75s Setting up gcc (4:14.1.0-2ubuntu1) ... 75s Setting up dh-autoreconf (20) ... 75s Setting up g++ (4:14.1.0-2ubuntu1) ... 75s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 75s Setting up build-essential (12.10ubuntu1) ... 75s Setting up debhelper (13.20ubuntu1) ... 75s Setting up autopkgtest-satdep (0) ... 75s Processing triggers for man-db (2.12.1-3) ... 77s Processing triggers for install-info (7.1.1-1) ... 77s Processing triggers for libc-bin (2.40-1ubuntu3) ... 80s (Reading database ... 80033 files and directories currently installed.) 80s Removing autopkgtest-satdep (0) ... 80s autopkgtest [12:43:16]: test autodep8-perl-build-deps: /usr/share/pkg-perl-autopkgtest/runner build-deps 80s autopkgtest [12:43:16]: test autodep8-perl-build-deps: [----------------------- 81s t/00load.t ....... 81s ok 1 - use Bio::DB::HTS; 81s ok 2 - use Bio::DB::HTS::Tabix; 81s ok 3 - use Bio::DB::HTS::Tabix::Iterator; 81s ok 4 - use Bio::DB::HTS::Kseq; 81s 1..4 81s ok 82s t/01bam.t ........ 82s 1..452 82s # Running under perl version 5.040000 for linux 82s # Current time local: Mon Nov 4 12:43:17 2024 82s # Current time GMT: Mon Nov 4 12:43:17 2024 82s # Using Test.pm version 1.31 82s ok 1 82s ok 2 82s ok 3 82s ok 4 82s ok 5 82s ok 6 82s ok 7 82s ok 8 82s ok 9 82s ok 10 82s ok 11 82s ok 12 82s ok 13 82s ok 14 82s ok 15 82s ok 16 82s ok 17 82s ok 18 82s ok 19 82s ok 20 82s ok 21 82s ok 22 82s ok 23 82s ok 24 82s ok 25 82s ok 26 82s ok 27 82s ok 28 82s ok 29 82s ok 30 82s ok 31 82s ok 32 82s ok 33 82s ok 34 82s ok 35 82s ok 36 82s ok 37 82s ok 38 82s ok 39 82s ok 40 82s ok 41 82s ok 42 82s ok 43 82s ok 44 82s ok 45 82s ok 46 82s ok 47 82s ok 48 82s ok 49 82s ok 50 82s ok 51 82s ok 52 82s ok 53 82s ok 54 82s ok 55 82s ok 56 82s ok 57 82s ok 58 82s ok 59 82s ok 60 82s ok 61 82s ok 62 82s ok 63 82s ok 64 82s ok 65 82s ok 66 82s ok 67 82s ok 68 82s ok 69 82s ok 70 82s ok 71 82s ok 72 82s ok 73 82s ok 74 82s ok 75 82s ok 76 82s ok 77 82s ok 78 82s ok 79 82s ok 80 82s ok 81 82s ok 82 82s ok 83 82s ok 84 82s ok 85 82s ok 86 82s ok 87 82s ok 88 82s ok 89 82s ok 90 82s ok 91 82s ok 92 82s ok 93 82s ok 94 82s ok 95 82s ok 96 82s ok 97 82s ok 98 82s ok 99 82s ok 100 82s ok 101 82s ok 102 82s ok 103 82s ok 104 82s ok 105 82s ok 106 82s ok 107 82s ok 108 82s ok 109 82s ok 110 82s ok 111 82s ok 112 82s ok 113 82s ok 114 82s ok 115 82s ok 116 82s ok 117 82s ok 118 82s ok 119 82s ok 120 82s ok 121 82s ok 122 82s ok 123 82s ok 124 82s ok 125 82s ok 126 82s ok 127 82s ok 128 82s ok 129 82s ok 130 82s ok 131 82s ok 132 82s ok 133 82s ok 134 82s ok 135 82s ok 136 82s ok 137 82s ok 138 82s ok 139 82s ok 140 82s ok 141 82s ok 142 82s ok 143 82s ok 144 82s ok 145 82s ok 146 82s ok 147 82s ok 148 82s ok 149 82s ok 150 82s ok 151 82s ok 152 82s ok 153 82s ok 154 82s ok 155 82s ok 156 82s ok 157 82s ok 158 82s ok 159 82s ok 160 82s ok 161 82s ok 162 82s ok 163 82s ok 164 82s ok 165 82s ok 166 82s ok 167 82s ok 168 82s ok 169 82s ok 170 82s ok 171 82s ok 172 82s ok 173 82s ok 174 82s ok 175 82s ok 176 82s ok 177 82s ok 178 82s ok 179 82s ok 180 82s ok 181 82s ok 182 82s ok 183 82s ok 184 82s ok 185 82s ok 186 82s ok 187 82s ok 188 82s ok 189 82s ok 190 82s ok 191 82s ok 192 82s ok 193 82s ok 194 82s ok 195 82s ok 196 82s ok 197 82s ok 198 82s ok 199 82s ok 200 82s ok 201 82s ok 202 82s ok 203 82s ok 204 82s ok 205 82s ok 206 82s ok 207 82s ok 208 82s ok 209 82s ok 210 82s ok 211 82s ok 212 82s ok 213 82s ok 214 82s ok 215 82s ok 216 82s ok 217 82s ok 218 82s ok 219 82s ok 220 82s ok 221 82s ok 222 82s ok 223 82s ok 224 82s ok 225 82s ok 226 82s ok 227 82s ok 228 82s ok 229 82s ok 230 82s ok 231 82s ok 232 82s ok 233 82s ok 234 82s ok 235 82s ok 236 82s ok 237 82s ok 238 82s ok 239 82s ok 240 82s ok 241 82s ok 242 82s ok 243 82s ok 244 82s ok 245 82s ok 246 82s ok 247 82s ok 248 82s ok 249 82s ok 250 82s ok 251 82s ok 252 82s ok 253 82s ok 254 82s ok 255 82s ok 256 82s ok 257 82s ok 258 82s ok 259 82s ok 260 82s ok 261 82s ok 262 82s ok 263 82s ok 264 82s ok 265 82s ok 266 82s ok 267 82s ok 268 82s ok 269 82s ok 270 82s ok 271 82s ok 272 82s ok 273 82s ok 274 82s ok 275 82s ok 276 82s ok 277 82s ok 278 82s ok 279 82s ok 280 82s ok 281 82s ok 282 82s ok 283 82s ok 284 82s ok 285 82s ok 286 82s ok 287 82s ok 288 82s ok 289 82s ok 290 82s ok 291 82s ok 292 82s ok 293 82s ok 294 82s ok 295 82s ok 296 82s ok 297 82s ok 298 82s ok 299 82s ok 300 82s ok 301 82s ok 302 82s ok 303 82s ok 304 82s ok 305 82s ok 306 82s ok 307 82s ok 308 82s ok 309 82s ok 310 82s ok 311 82s ok 312 82s ok 313 82s ok 314 82s ok 315 82s ok 316 82s ok 317 82s ok 318 82s ok 319 82s ok 320 82s ok 321 82s ok 322 82s ok 323 82s ok 324 82s ok 325 82s ok 326 82s ok 327 82s ok 328 82s ok 329 82s ok 330 82s ok 331 82s ok 332 82s ok 333 82s ok 334 82s ok 335 82s ok 336 82s ok 337 82s ok 338 82s ok 339 82s ok 340 82s ok 341 82s ok 342 82s ok 343 82s ok 344 82s ok 345 82s ok 346 82s ok 347 82s ok 348 82s ok 349 82s ok 350 82s ok 351 82s ok 352 82s ok 353 82s ok 354 82s ok 355 82s ok 356 82s ok 357 82s ok 358 82s ok 359 82s ok 360 82s ok 361 82s ok 362 82s ok 363 82s ok 364 82s ok 365 82s ok 366 82s ok 367 82s ok 368 82s ok 369 82s ok 370 82s ok 371 82s ok 372 82s ok 373 82s ok 374 82s ok 375 82s ok 376 82s ok 377 82s ok 378 82s ok 379 82s ok 380 82s ok 381 82s ok 382 82s ok 383 82s ok 384 82s ok 385 82s ok 386 82s ok 387 82s ok 388 82s ok 389 82s ok 390 82s ok 391 82s ok 392 82s ok 393 82s ok 394 82s ok 395 82s ok 396 82s ok 397 82s ok 398 82s ok 399 82s ok 400 82s ok 401 82s ok 402 82s ok 403 82s ok 404 82s ok 405 82s ok 406 82s ok 407 82s ok 408 82s ok 409 82s ok 410 82s ok 411 82s ok 412 82s ok 413 82s ok 414 82s ok 415 82s ok 416 82s ok 417 82s ok 418 82s ok 419 82s ok 420 82s ok 421 82s ok 422 82s ok 423 82s ok 424 82s ok 425 82s ok 426 82s ok 427 82s ok 428 82s ok 429 82s ok 430 82s ok 431 82s ok 432 82s ok 433 82s ok 434 82s ok 435 82s ok 436 82s ok 437 82s ok 438 82s ok 439 82s ok 440 82s ok 441 82s ok 442 82s ok 443 82s ok 444 82s ok 445 82s ok 446 82s ok 447 82s ok 448 82s ok 449 82s ok 450 82s ok 451 82s ok 452 82s ok 82s t/02faidx.t ...... 82s 1..15 82s ok 1 - use Bio::DB::HTS; 82s ok 2 - use Bio::DB::HTS::Faidx; 82s ok 3 82s ok 4 82s ok 5 82s ok 6 82s ok 7 82s ok 8 82s ok 9 82s ok 10 82s ok 11 82s ok 12 82s # 230218 82s ok 13 - length of I 82s ok 14 - has sequence I 82s ok 15 - Does not have sequence II 82s ok 85s t/03cram.t ....... 85s 1..139 85s # Running under perl version 5.040000 for linux 85s # Current time local: Mon Nov 4 12:43:18 2024 85s # Current time GMT: Mon Nov 4 12:43:18 2024 85s # Using Test.pm version 1.31 85s ok 1 85s ok 2 85s ok 3 85s ok 4 85s ok 5 85s ok 6 85s ok 7 85s ok 8 85s ok 9 85s ok 10 85s ok 11 85s ok 12 85s ok 13 85s ok 14 85s ok 15 85s ok 16 85s ok 17 85s ok 18 85s ok 19 85s ok 20 85s ok 21 85s ok 22 85s ok 23 85s ok 24 85s ok 25 85s ok 26 85s ok 27 85s ok 28 85s ok 29 85s ok 30 85s ok 31 85s ok 32 85s ok 33 85s ok 34 85s ok 35 85s ok 36 85s ok 37 85s ok 38 85s ok 39 85s ok 40 85s ok 41 85s ok 42 85s ok 43 85s ok 44 85s ok 45 85s ok 46 85s ok 47 85s ok 48 85s ok 49 85s ok 50 85s ok 51 85s ok 52 85s ok 53 85s ok 54 85s ok 55 85s ok 56 85s ok 57 85s ok 58 85s ok 59 85s ok 60 85s ok 61 85s ok 62 85s ok 63 85s ok 64 85s ok 65 85s ok 66 85s ok 67 85s ok 68 85s ok 69 85s ok 70 85s ok 71 85s ok 72 85s ok 73 85s ok 74 85s ok 75 85s ok 76 85s ok 77 85s ok 78 85s ok 79 85s ok 80 85s ok 81 85s ok 82 85s ok 83 85s ok 84 85s ok 85 85s ok 86 85s ok 87 85s ok 88 85s ok 89 85s ok 90 85s ok 91 85s ok 92 85s ok 93 85s ok 94 85s ok 95 85s ok 96 85s ok 97 85s ok 98 85s ok 99 85s ok 100 85s ok 101 85s ok 102 85s ok 103 85s ok 104 85s ok 105 85s ok 106 85s ok 107 85s ok 108 85s ok 109 85s ok 110 85s ok 111 85s ok 112 85s ok 113 85s ok 114 85s ok 115 85s ok 116 85s ok 117 85s ok 118 85s ok 119 85s ok 120 85s ok 121 85s ok 122 85s ok 123 85s ok 124 85s ok 125 85s ok 126 85s ok 127 85s ok 128 85s ok 129 85s ok 130 85s ok 131 85s ok 132 85s ok 133 85s ok 134 85s ok 135 85s ok 136 85s ok 137 85s ok 138 85s ok 139 85s ok 85s t/04tabix.t ...... 85s 1..21 85s ok 1 - use Bio::DB::HTS::Tabix; 85s ok 2 - \#CHROM FROM TO GERP 85s ok 3 - \#CHROM FROM TO GERP 85s ok 4 - can query a region 85s ok 5 - can get a value from the iterator 85s ok 6 - row value is correct 85s ok 7 - correct number of values come back from the iterator 85s ok 8 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 9 - seqnames are correct 85s ok 10 - can query a region with ':' in chr 85s ok 11 - can get a value from the iterator 85s ok 12 - row value is correct with ':' in chr 85s ok 13 - can query a region with ':' in chr, no end 85s ok 14 - can get a value from the iterator 85s ok 15 - row value is correct with ':' in chr, no end 85s ok 16 - can query a region with ':' in chr, no coord 85s ok 17 - can get a value from the iterator 85s ok 18 - row value is correct with ':' in chr, no coord 85s ok 19 - querying non existent chrom 85s ok 20 - \#\#fileformat=VCFv4.2 85s ok 21 - \#\#reference=human_b36_both.fasta 85s ok 85s t/05vcf.t ........ 85s 1..177 85s ok 1 - use Bio::DB::HTS::VCF; 85s ok 2 - use Bio::DB::HTS::VCF::Row; 85s ok 3 - use Bio::DB::HTS::VCF::RowPtr; 85s ok 4 - use Bio::DB::HTS::VCF::Header; 85s ok 5 - use Bio::DB::HTS::VCF::HeaderPtr; 85s ok 6 - Chromosome value read 85s ok 7 - Chromosome value read 85s ok 8 - Position value read 85s ok 9 - Quality value read 85s ok 10 - Quality value read 85s ok 11 - ID value read 85s ok 12 - Number of alleles value read 85s ok 13 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 14 - alleles are correct 85s ok 15 - VCF file open 85s ok 16 - correct number of variants identified in file 85s ok 17 - Header formatted string 85s ok 18 - VCF Header version matches 85s ok 19 - Number of samples 85s ok 20 - sample names correct 85s ok 21 - Number of seqnames 85s ok 22 85s ok 23 - sequence names correct 85s ok 24 - Next row 85s ok 25 - Chromosome value read 85s ok 26 - Position value read 85s ok 27 - ID value read 85s ok 28 - Num Filters OK 85s ok 29 - Actual Filter present 85s ok 30 - PASS filter absent 85s ok 31 - Variant type matches 85s ok 32 - info read correctly 85s ok 33 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 34 - info flag read correctly 85s ok 35 - info flag type correct 85s ok 36 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 37 - info float read correctly 85s ok 38 - info float type correct 85s ok 39 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 40 - info string read correctly 85s ok 41 - info String type correct 85s ok 42 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 43 - info ints read correctly 85s ok 44 - info int type correct 85s ok 45 - format int read 85s ok 46 - format int read 85s ok 47 - format id not present 85s ok 48 - format read 85s ok 49 - Next row 85s ok 50 - Chromosome value read 85s ok 51 - Position value read 85s ok 52 - Quality value read 85s ok 53 - Reference value read 85s ok 54 - Num Alleles 85s ok 55 - Is SNP 85s ok 56 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 57 - alleles are correct 85s ok 58 - Num Filters OK 85s ok 59 - PASS Filter present 85s ok 60 - Actual Filter absent 85s ok 61 - Made up filter not existing 85s ok 62 - info read correctly 85s ok 63 - format int read 85s ok 64 - format int read 85s ok 65 - format id not present 85s ok 66 - format read 85s ok 67 - Next row 85s ok 68 - Chromosome value read 85s ok 69 - int format type correct 85s ok 70 - format int read 85s ok 71 - format int read 85s ok 72 - format int read 85s # !!! Not sure this is correct !!! 85s ok 73 - format int read 85s ok 74 - format read 85s ok 75 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 76 - genotypes read correctly 85s ok 77 - format id not found 85s ok 78 - info id not found 85s ok 79 - info read correctly 85s ok 80 - can query a region 85s ok 81 - can get a value from the iterator 85s ok 82 - chr 85s ok 83 - position 85s ok 84 - id 85s ok 85 - reference 85s ok 86 - info 85s ok 87 - info 85s ok 88 - info 85s ok 89 - info 85s ok 90 - can get a value from the iterator 85s ok 91 - chr 85s ok 92 - position 85s ok 93 - id 85s ok 94 - reference 85s ok 95 - info 85s ok 96 - no more results 85s ok 97 - BCF file open 85s ok 98 - correct number of variants identified in file 85s ok 99 - Header formatted string 85s ok 100 - VCF Header version matches 85s ok 101 - Number of samples 85s ok 102 - sample names correct 85s ok 103 - Number of seqnames 85s ok 104 - sequence names correct 85s ok 105 - Next row 85s ok 106 - Chromosome value read 85s ok 107 - Position value read 85s ok 108 - ID value read 85s ok 109 - Num Filters OK 85s ok 110 - Actual Filter present 85s ok 111 - PASS filter absent 85s ok 112 - Variant type matches 85s ok 113 - info read correctly 85s ok 114 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 115 - info flag read correctly 85s ok 116 - info flag type correct 85s ok 117 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 118 - info float read correctly 85s ok 119 - info float type correct 85s ok 120 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 121 - info string read correctly 85s ok 122 - info String type correct 85s ok 123 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 124 - info ints read correctly 85s ok 125 - info int type correct 85s ok 126 - format int read 85s ok 127 - format int read 85s ok 128 - format ID not present 85s ok 129 - format read 85s ok 130 - Next row 85s ok 131 - Chromosome value read 85s ok 132 - Position value read 85s ok 133 - Quality value read 85s ok 134 - Reference value read 85s ok 135 - Num Alleles 85s ok 136 - Is SNP 85s ok 137 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 138 - alleles are correct 85s ok 139 - Num Filters OK 85s ok 140 - PASS Filter present 85s ok 141 - Actual Filter absent 85s ok 142 - Made up filter not existing 85s ok 143 - info read correctly 85s ok 144 - format int read 85s ok 145 - format int read 85s ok 146 - format ID not present 85s ok 147 - format read 85s ok 148 - Next row 85s ok 149 - Chromosome value read 85s ok 150 - int format type correct 85s ok 151 - format int read 85s ok 152 - format int read 85s ok 153 - format int read 85s # !!! Not sure this is correct !!! 85s ok 154 - format int read 85s ok 155 - format read 85s ok 156 - A reference of type 'ARRAY' isa 'ARRAY' 85s ok 157 - genotypes read correctly 85s ok 158 - format id not found 85s ok 159 - info id not found 85s ok 160 - info read correctly 85s ok 161 - can query a region 85s ok 162 - can get a value from the iterator 85s ok 163 - chr 85s ok 164 - position 85s ok 165 - id 85s ok 166 - reference 85s ok 167 - info 85s ok 168 - info 85s ok 169 - info 85s ok 170 - info 85s ok 171 - can get a value from the iterator 85s ok 172 - chr 85s ok 173 - position 85s ok 174 - id 85s ok 175 - reference 85s ok 176 - info 85s ok 177 - no more results 85s ok 85s t/06kseq.t ....... 85s ok 1 - correct num. seqs in bug2335 85s ok 2 - sample sequence obtained 85s ok 3 - seq matches bug2335 85s ok 4 - desc matches bug2335 85s ok 5 - name matches bug2335 85s ok 6 - qual matches bug2335 85s ok 7 - Checking qual and seq lengths are the same in bug2335 85s ok 8 - Checking qual and seq lengths are the same using object methods in bug2335 85s ok 9 - correct num. seqs in evil_wrapping 85s ok 10 - sample sequence obtained 85s ok 11 - seq matches evil_wrapping 85s ok 12 - desc matches evil_wrapping 85s ok 13 - name matches evil_wrapping 85s ok 14 - qual matches evil_wrapping 85s ok 15 - Checking qual and seq lengths are the same in evil_wrapping 85s ok 16 - Checking qual and seq lengths are the same using object methods in evil_wrapping 85s ok 17 - correct num. seqs in example 85s ok 18 - sample sequence obtained 85s ok 19 - seq matches example 85s ok 20 - desc matches example 85s ok 21 - name matches example 85s ok 22 - qual matches example 85s ok 23 - Checking qual and seq lengths are the same in example 85s ok 24 - Checking qual and seq lengths are the same using object methods in example 85s ok 25 - correct num. seqs in illumina_faked 85s ok 26 - sample sequence obtained 85s ok 27 - seq matches illumina_faked 85s ok 28 - desc matches illumina_faked 85s ok 29 - name matches illumina_faked 85s ok 30 - qual matches illumina_faked 85s ok 31 - Checking qual and seq lengths are the same in illumina_faked 85s ok 32 - Checking qual and seq lengths are the same using object methods in illumina_faked 85s ok 33 - correct num. seqs in sanger_93 85s ok 34 - sample sequence obtained 85s ok 35 - seq matches sanger_93 85s ok 36 - desc matches sanger_93 85s ok 37 - name matches sanger_93 85s ok 38 - qual matches sanger_93 85s ok 39 - Checking qual and seq lengths are the same in sanger_93 85s ok 40 - Checking qual and seq lengths are the same using object methods in sanger_93 85s ok 41 - correct num. seqs in sanger_faked 85s ok 42 - sample sequence obtained 85s ok 43 - seq matches sanger_faked 85s ok 44 - desc matches sanger_faked 85s ok 45 - name matches sanger_faked 85s ok 46 - qual matches sanger_faked 85s ok 47 - Checking qual and seq lengths are the same in sanger_faked 85s ok 48 - Checking qual and seq lengths are the same using object methods in sanger_faked 85s ok 49 - correct num. seqs in solexa_example 85s ok 50 - sample sequence obtained 85s ok 51 - seq matches solexa_example 85s ok 52 - desc matches solexa_example 85s ok 53 - name matches solexa_example 85s ok 54 - qual matches solexa_example 85s ok 55 - Checking qual and seq lengths are the same in solexa_example 85s ok 56 - Checking qual and seq lengths are the same using object methods in solexa_example 85s ok 57 - correct num. seqs in solexa_faked 85s ok 58 - sample sequence obtained 85s ok 59 - seq matches solexa_faked 85s ok 60 - desc matches solexa_faked 85s ok 61 - name matches solexa_faked 85s ok 62 - qual matches solexa_faked 85s ok 63 - Checking qual and seq lengths are the same in solexa_faked 85s ok 64 - Checking qual and seq lengths are the same using object methods in solexa_faked 85s ok 65 - correct num. seqs in test1_sanger 85s ok 66 - sample sequence obtained 85s ok 67 - seq matches test1_sanger 85s ok 68 - desc matches test1_sanger 85s ok 69 - name matches test1_sanger 85s ok 70 - qual matches test1_sanger 85s ok 71 - Checking qual and seq lengths are the same in test1_sanger 85s ok 72 - Checking qual and seq lengths are the same using object methods in test1_sanger 85s ok 73 - correct num. seqs in test2_solexa 85s ok 74 - sample sequence obtained 85s ok 75 - seq matches test2_solexa 85s ok 76 - desc matches test2_solexa 85s ok 77 - name matches test2_solexa 85s ok 78 - qual matches test2_solexa 85s ok 79 - Checking qual and seq lengths are the same in test2_solexa 85s ok 80 - Checking qual and seq lengths are the same using object methods in test2_solexa 85s ok 81 - correct num. seqs in test3_illumina 85s ok 82 - sample sequence obtained 85s ok 83 - seq matches test3_illumina 85s ok 84 - desc matches test3_illumina 85s ok 85 - name matches test3_illumina 85s ok 86 - qual matches test3_illumina 85s ok 87 - Checking qual and seq lengths are the same in test3_illumina 85s ok 88 - Checking qual and seq lengths are the same using object methods in test3_illumina 85s ok 89 - correct num. seqs in tricky 85s ok 90 - sample sequence obtained 85s ok 91 - seq matches tricky 85s ok 92 - desc matches tricky 85s ok 93 - name matches tricky 85s ok 94 - qual matches tricky 85s ok 95 - Checking qual and seq lengths are the same in tricky 85s ok 96 - Checking qual and seq lengths are the same using object methods in tricky 85s ok 97 - correct num. seqs in zero_qual 85s ok 98 - sample sequence obtained 85s ok 99 - seq matches zero_qual 85s ok 100 - desc matches zero_qual 85s ok 101 - name matches zero_qual 85s ok 102 - qual matches zero_qual 85s ok 103 - Checking qual and seq lengths are the same in zero_qual 85s ok 104 - Checking qual and seq lengths are the same using object methods in zero_qual 85s 1..104 85s ok 86s t/07cramwrite.t .. 86s 1..22 86s # Running under perl version 5.040000 for linux 86s # Current time local: Mon Nov 4 12:43:21 2024 86s # Current time GMT: Mon Nov 4 12:43:21 2024 86s # Using Test.pm version 1.31 86s ok 1 86s ok 2 86s ok 3 86s ok 4 86s ok 5 86s ok 6 86s ok 7 86s ok 8 86s ok 9 86s ok 10 86s ok 11 86s ok 12 86s ok 13 86s ok 14 86s ok 15 86s ok 16 86s ok 17 86s ok 18 86s ok 19 86s ok 20 86s ok 21 86s ok 22 86s ok 86s t/08bamwrite.t ... 86s 1..22 86s # Running under perl version 5.040000 for linux 86s # Current time local: Mon Nov 4 12:43:22 2024 86s # Current time GMT: Mon Nov 4 12:43:22 2024 86s # Using Test.pm version 1.31 86s ok 1 86s ok 2 86s ok 3 86s ok 4 86s ok 5 86s ok 6 86s ok 7 86s ok 8 86s ok 9 86s ok 10 86s ok 11 86s ok 12 86s ok 13 86s ok 14 86s ok 15 86s ok 16 86s ok 17 86s ok 18 86s ok 19 86s ok 20 86s ok 21 86s ok 22 86s ok 86s t/09sam.t ........ 86s ok 1 86s ok 2 # skip Cannot test header reading for htslib < 1.5 86s ok 3 # skip Cannot test header reading for htslib < 1.5 86s ok 4 # skip Cannot test header reading for htslib < 1.5 86s ok 5 # skip Cannot test header reading for htslib < 1.5 86s ok 6 # skip Cannot test header reading for htslib < 1.5 86s ok 7 # skip Cannot test header reading for htslib < 1.5 86s ok 8 # skip Cannot test header reading for htslib < 1.5 86s ok 9 # skip Cannot test header reading for htslib < 1.5 86s ok 10 # skip Cannot test header reading for htslib < 1.5 86s ok 11 # skip Cannot test header reading for htslib < 1.5 86s ok 12 86s ok 13 86s ok 14 # skip Cannot test iterating over alignments for htslib < 1.5 86s ok 15 # skip Cannot test iterating over alignments for htslib < 1.5 86s ok 16 # skip Cannot test iterating over alignments for htslib < 1.5 86s ok 17 # skip Cannot test iterating over alignments for htslib < 1.5 86s ok 18 86s ok 19 86s ok 20 86s ok 21 86s ok 22 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' 86s ok 23 86s 1..23 86s ok 86s t/10leak.t ....... skipped: require Test::LeakTrace 86s All tests successful. 86s Files=11, Tests=979, 5 wallclock secs ( 0.06 usr 0.02 sys + 4.62 cusr 0.49 csys = 5.19 CPU) 86s Result: PASS 86s autopkgtest [12:43:22]: test autodep8-perl-build-deps: -----------------------] 87s autodep8-perl-build-deps PASS 87s autopkgtest [12:43:23]: test autodep8-perl-build-deps: - - - - - - - - - - results - - - - - - - - - - 87s autopkgtest [12:43:23]: test autodep8-perl: preparing testbed 1356s autopkgtest [13:04:32]: testbed dpkg architecture: amd64 1356s autopkgtest [13:04:32]: testbed apt version: 2.9.8 1356s autopkgtest [13:04:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1357s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1357s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 1357s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1357s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 1357s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 1357s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 1357s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 1357s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 1357s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 1357s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 1357s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 1357s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 1357s Fetched 5618 kB in 1s (9354 kB/s) 1357s Reading package lists... 1359s Reading package lists... 1359s Building dependency tree... 1359s Reading state information... 1359s Calculating upgrade... 1360s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1360s Reading package lists... 1360s Building dependency tree... 1360s Reading state information... 1360s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1360s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1360s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1360s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1360s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1361s Reading package lists... 1361s Reading package lists... 1362s Building dependency tree... 1362s Reading state information... 1362s Calculating upgrade... 1362s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1362s Reading package lists... 1362s Building dependency tree... 1362s Reading state information... 1363s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1364s Reading package lists... 1364s Building dependency tree... 1364s Reading state information... 1365s Starting pkgProblemResolver with broken count: 0 1365s Starting 2 pkgProblemResolver with broken count: 0 1365s Done 1365s The following additional packages will be installed: 1365s autodep8 dctrl-tools libbio-db-hts-perl libbio-perl-perl libdata-stag-perl 1365s libdeflate0 libhts3t64 libhtscodecs2 libio-string-perl pkg-perl-autopkgtest 1365s Suggested packages: 1365s debtags bioperl libxml-sax-expatxs-perl 1365s Recommended packages: 1365s bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl 1365s libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl 1365s libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl 1365s libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl 1365s libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl 1365s libset-scalar-perl libsoap-lite-perl libsort-naturally-perl 1365s libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl 1365s libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl 1365s libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl 1365s libxml-writer-perl libxml-libxml-perl libwww-perl perl-tk libgd-gd2-perl 1365s | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl 1365s The following NEW packages will be installed: 1365s autodep8 autopkgtest-satdep dctrl-tools libbio-db-hts-perl libbio-perl-perl 1365s libdata-stag-perl libdeflate0 libhts3t64 libhtscodecs2 libio-string-perl 1365s pkg-perl-autopkgtest 1365s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 1365s Need to get 3893 kB/3894 kB of archives. 1365s After this operation, 12.0 MB of additional disk space will be used. 1365s Get:1 /tmp/autopkgtest.efi4EO/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 1365s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 1365s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 autodep8 all 0.28+nmu1ubuntu1 [13.7 kB] 1365s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 1365s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 1365s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 1365s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 1365s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdata-stag-perl all 0.14-3 [372 kB] 1365s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbio-perl-perl all 1.7.8-1 [2580 kB] 1365s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbio-db-hts-perl amd64 3.01-4build4 [141 kB] 1365s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-perl-autopkgtest all 0.79 [18.5 kB] 1366s Fetched 3893 kB in 0s (40.4 MB/s) 1366s Selecting previously unselected package dctrl-tools. 1366s (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 ... 75323 files and directories currently installed.) 1366s Preparing to unpack .../00-dctrl-tools_2.24-3build3_amd64.deb ... 1366s Unpacking dctrl-tools (2.24-3build3) ... 1366s Selecting previously unselected package autodep8. 1366s Preparing to unpack .../01-autodep8_0.28+nmu1ubuntu1_all.deb ... 1366s Unpacking autodep8 (0.28+nmu1ubuntu1) ... 1366s Selecting previously unselected package libdeflate0:amd64. 1366s Preparing to unpack .../02-libdeflate0_1.21-1_amd64.deb ... 1366s Unpacking libdeflate0:amd64 (1.21-1) ... 1366s Selecting previously unselected package libhtscodecs2:amd64. 1366s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_amd64.deb ... 1366s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 1366s Selecting previously unselected package libhts3t64:amd64. 1366s Preparing to unpack .../04-libhts3t64_1.20+ds-2_amd64.deb ... 1366s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 1366s Selecting previously unselected package libio-string-perl. 1366s Preparing to unpack .../05-libio-string-perl_1.08-4_all.deb ... 1366s Unpacking libio-string-perl (1.08-4) ... 1366s Selecting previously unselected package libdata-stag-perl. 1366s Preparing to unpack .../06-libdata-stag-perl_0.14-3_all.deb ... 1366s Unpacking libdata-stag-perl (0.14-3) ... 1366s Selecting previously unselected package libbio-perl-perl. 1366s Preparing to unpack .../07-libbio-perl-perl_1.7.8-1_all.deb ... 1366s Unpacking libbio-perl-perl (1.7.8-1) ... 1366s Selecting previously unselected package libbio-db-hts-perl. 1366s Preparing to unpack .../08-libbio-db-hts-perl_3.01-4build4_amd64.deb ... 1366s Unpacking libbio-db-hts-perl (3.01-4build4) ... 1366s Selecting previously unselected package pkg-perl-autopkgtest. 1366s Preparing to unpack .../09-pkg-perl-autopkgtest_0.79_all.deb ... 1366s Unpacking pkg-perl-autopkgtest (0.79) ... 1366s Selecting previously unselected package autopkgtest-satdep. 1366s Preparing to unpack .../10-2-autopkgtest-satdep.deb ... 1366s Unpacking autopkgtest-satdep (0) ... 1366s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 1366s Setting up libdeflate0:amd64 (1.21-1) ... 1366s Setting up libio-string-perl (1.08-4) ... 1366s Setting up libdata-stag-perl (0.14-3) ... 1366s Setting up libhts3t64:amd64 (1.20+ds-2) ... 1366s Setting up libbio-perl-perl (1.7.8-1) ... 1366s Setting up dctrl-tools (2.24-3build3) ... 1366s Setting up autodep8 (0.28+nmu1ubuntu1) ... 1366s Setting up libbio-db-hts-perl (3.01-4build4) ... 1366s Setting up pkg-perl-autopkgtest (0.79) ... 1366s Setting up autopkgtest-satdep (0) ... 1366s Processing triggers for man-db (2.12.1-3) ... 1368s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1370s (Reading database ... 76676 files and directories currently installed.) 1370s Removing autopkgtest-satdep (0) ... 1371s autopkgtest [13:04:47]: test autodep8-perl: /usr/share/pkg-perl-autopkgtest/runner runtime-deps 1371s autopkgtest [13:04:47]: test autodep8-perl: [----------------------- 1372s /usr/share/pkg-perl-autopkgtest/runtime-deps.d/use.t .. 1372s 1..4 1372s ok 1 - /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 exited successfully 1372s ok 2 - /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 produced no (non-whitelisted) output 1372s ok 3 - env PERL_DL_NONLAZY=1 /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 exited successfully 1372s ok 4 - env PERL_DL_NONLAZY=1 /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 produced no (non-whitelisted) output 1372s ok 1372s All tests successful. 1372s Files=1, Tests=4, 1 wallclock secs ( 0.01 usr 0.01 sys + 0.19 cusr 0.05 csys = 0.26 CPU) 1372s Result: PASS 1372s autopkgtest [13:04:48]: test autodep8-perl: -----------------------] 1372s autodep8-perl PASS (superficial) 1372s autopkgtest [13:04:48]: test autodep8-perl: - - - - - - - - - - results - - - - - - - - - - 1372s autopkgtest [13:04:48]: test autodep8-perl-recommends: preparing testbed 1373s Reading package lists... 1373s Building dependency tree... 1373s Reading state information... 1374s Starting pkgProblemResolver with broken count: 0 1374s Starting 2 pkgProblemResolver with broken count: 0 1374s Done 1374s The following NEW packages will be installed: 1374s autopkgtest-satdep 1374s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1374s Need to get 0 B/720 B of archives. 1374s After this operation, 0 B of additional disk space will be used. 1374s Get:1 /tmp/autopkgtest.efi4EO/3-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 1375s Selecting previously unselected package autopkgtest-satdep. 1375s (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 ... 76676 files and directories currently installed.) 1375s Preparing to unpack .../3-autopkgtest-satdep.deb ... 1375s Unpacking autopkgtest-satdep (0) ... 1375s Setting up autopkgtest-satdep (0) ... 1376s (Reading database ... 76676 files and directories currently installed.) 1376s Removing autopkgtest-satdep (0) ... 1377s autopkgtest [13:04:53]: test autodep8-perl-recommends: /usr/share/pkg-perl-autopkgtest/runner runtime-deps-and-recommends 1377s autopkgtest [13:04:53]: test autodep8-perl-recommends: [----------------------- 1378s /usr/share/pkg-perl-autopkgtest/runtime-deps-and-recommends.d/syntax.t .. 1378s 1..4 1378s ok 1 - Package libbio-db-hts-perl is known to dpkg 1378s ok 2 - Got status information for package libbio-db-hts-perl 1378s ok 3 - Got file list for package libbio-db-hts-perl 1378s # Subtest: all modules in libbio-db-hts-perl pass the syntax check 1378s 1..22 1378s ok 1 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/AlignWrapper.pm exited successfully 1378s # Subroutine each_tag_value redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 461. 1378s # Subroutine get_tag_values redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 463. 1378s # Subroutine has_tag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 479. 1378s # Subroutine get_all_tags redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 495. 1378s # Subroutine start redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 502. 1378s # Subroutine end redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 508. 1378s # Subroutine stop redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 514. 1378s # Subroutine strand redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 517. 1378s # Subroutine abs_strand redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 521. 1378s # Subroutine mstrand redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 523. 1378s # Subroutine display_name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 528. 1378s # Subroutine qscore redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 532. 1378s # Subroutine qstring redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 539. 1378s # Subroutine primary_id redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 543. 1378s # Subroutine cigar_str redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 550. 1378s # Subroutine cigar_array redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 563. 1378s # Subroutine flag_str redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 577. 1378s # Subroutine length redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 586. 1378s # Subroutine mate_start redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 593. 1378s # Subroutine mate_len redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 599. 1378s # Subroutine mate_end redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 618. 1378s # Subroutine query redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 624. 1378s # Subroutine get_SeqFeatures redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 629. 1378s # Subroutine target redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 633. 1378s # Subroutine primary_tag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 638. 1378s # Subroutine source_tag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 639. 1378s # Subroutine hit redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 641. 1378s ok 2 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm exited successfully 1378s ok 3 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Constants.pm exited successfully 1378s ok 4 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Faidx.pm exited successfully 1378s ok 5 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/FetchIterator.pm exited successfully 1378s ok 6 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Record.pm exited successfully 1378s ok 7 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq.pm exited successfully 1378s ok 8 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Pileup.pm exited successfully 1378s ok 9 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/PileupWrapper.pm exited successfully 1378s # Constant subroutine Bio::DB::HTS::Query::CIGAR_SKIP redefined at /usr/lib/x86_64-linux-gnu/perl-base/constant.pm line 171. 1378s # Subroutine new redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 64. 1378s # Subroutine seq_id redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 76. 1378s # Subroutine name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 87. 1378s # Subroutine display_name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 98. 1378s # Subroutine primary_tag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 106. 1378s # Subroutine source_tag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 114. 1378s # Subroutine start redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 122. 1378s # Subroutine end redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 133. 1378s # Subroutine low redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 138. 1378s # Subroutine high redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 150. 1378s # Subroutine length redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 171. 1378s # Subroutine seq redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 184. 1378s # Subroutine qscore redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 198. 1378s # Subroutine dna redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 210. 1378s # Subroutine strand redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 221. 1378s # Subroutine subseq redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 233. 1378s ok 10 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm exited successfully 1378s ok 11 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/ReadIterator.pm exited successfully 1378s # Name "Bio::DB::HTS::Segment::ref" used only once: possible typo at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm line 70. 1378s # Name "Bio::DB::HTS::Segment::abs_ref" used only once: possible typo at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm line 70. 1378s # Name "Bio::DB::HTS::Segment::sourceseq" used only once: possible typo at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm line 70. 1378s ok 12 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm exited successfully 1378s ok 13 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix/Iterator.pm exited successfully 1378s ok 14 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix.pm exited successfully 1378s # Subroutine dna redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 43. 1378s # Subroutine qscore redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 49. 1378s # Subroutine start redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 56. 1378s # Subroutine end redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 61. 1378s # Subroutine reversec redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 68. 1378s ok 15 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm exited successfully 1378s ok 16 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Header.pm exited successfully 1378s ok 17 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/HeaderPtr.pm exited successfully 1378s ok 18 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Iterator.pm exited successfully 1378s ok 19 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Row.pm exited successfully 1378s ok 20 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/RowPtr.pm exited successfully 1378s ok 21 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF.pm exited successfully 1378s # Constant subroutine Bio::DB::HTS::DUMP_INTERVAL redefined at /usr/lib/x86_64-linux-gnu/perl-base/constant.pm line 171. 1378s # Subroutine new redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1375. 1378s # Subroutine hts_file redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1409. 1378s # Subroutine clone redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1412. 1378s # Subroutine header redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1420. 1378s # Subroutine hts_path redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1426. 1378s # Subroutine fai redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1431. 1378s # Subroutine new_dna_accessor redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1433. 1378s # Subroutine can_do_seq redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1455. 1378s # Subroutine seq redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1462. 1378s # Subroutine expand_flags redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1473. 1378s # Subroutine split_splices redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1480. 1378s # Subroutine autoindex redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1487. 1378s # Subroutine force_refseq redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1494. 1378s # Subroutine n_targets redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1501. 1378s # Subroutine target_name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1505. 1378s # Subroutine target_len redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1512. 1378s # Subroutine seq_ids redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1519. 1378s # Subroutine _cache_targets redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1524. 1378s # Subroutine length redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1535. 1378s # Subroutine _fetch redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1541. 1378s # Subroutine fetch redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1554. 1378s # Subroutine pileup redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1566. 1378s # Subroutine fast_pileup redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1588. 1378s # Subroutine segment redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1611. 1378s # Subroutine get_features_by_location redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1636. 1378s # Subroutine get_features_by_attribute redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1652. 1378s # Subroutine get_features_by_tag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1658. 1378s # Subroutine get_features_by_flag redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1662. 1378s # Subroutine get_feature_by_name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1666. 1378s # Subroutine get_features_by_name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1678. 1378s # Subroutine get_feature_by_id redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1680. 1378s # Subroutine get_seq_stream redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1698. 1378s # Subroutine get_seq_fh redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1703. 1378s # Subroutine types redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1708. 1378s # Subroutine features redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1712. 1378s # Subroutine coverage2BedGraph redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1816. 1378s # Subroutine _filter_features redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1860. 1378s # Subroutine _push_features redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1904. 1378s # Subroutine last_feature_count redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1928. 1378s # Subroutine _features redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1930. 1378s # Subroutine _build_mates redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1950. 1378s # Subroutine _coverage redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2000. 1378s # Subroutine _segment_search redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2038. 1378s # Subroutine hts_index redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2053. 1378s # Subroutine _features_fh redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2062. 1378s # Subroutine tam_fh redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2076. 1378s # Subroutine max_pileup_cnt redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2081. 1378s # Subroutine _filter_by_name redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2088. 1378s # Subroutine _filter_by_attribute redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2104. 1378s # Subroutine _glob_match redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2132. 1378s # Subroutine open redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2146. 1378s # Subroutine seq redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2148. 1378s # Subroutine coverage redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2163. 1378s # Subroutine source redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2169. 1378s # Subroutine method redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2176. 1378s # Subroutine gff3_string redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2183. 1378s # Subroutine index redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2199. 1378s # Ambiguous call resolved as CORE::open(), qualify as such or use & at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2238. 1378s # Ambiguous call resolved as CORE::open(), qualify as such or use & at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2243. 1378s # Subroutine reindex redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2230. 1378s # Subroutine index_open_in_safewd redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2269. 1378s # Subroutine mtime redefined at /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2280. 1378s ok 22 - /usr/bin/perl -wc /usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm exited successfully 1378s ok 4 - all modules in libbio-db-hts-perl pass the syntax check 1378s ok 1378s All tests successful. 1378s Files=1, Tests=4, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.91 cusr 0.27 csys = 1.20 CPU) 1378s Result: PASS 1378s autopkgtest [13:04:54]: test autodep8-perl-recommends: -----------------------] 1379s autodep8-perl-recommends PASS (superficial) 1379s autopkgtest [13:04:55]: test autodep8-perl-recommends: - - - - - - - - - - results - - - - - - - - - - 1379s autopkgtest [13:04:55]: @@@@@@@@@@@@@@@@@@@@ summary 1379s autodep8-perl-build-deps PASS 1379s autodep8-perl PASS (superficial) 1379s autodep8-perl-recommends PASS (superficial) 1390s nova [W] Skipping flock for amd64 1390s Creating nova instance adt-plucky-amd64-libbio-db-hts-perl-20241104-124156-juju-7f2275-prod-proposed-migration-environment-2-8b0bee51-dd16-47a2-9247-23f6907eb5c2 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)... 1390s nova [W] Skipping flock for amd64 1390s Creating nova instance adt-plucky-amd64-libbio-db-hts-perl-20241104-124156-juju-7f2275-prod-proposed-migration-environment-2-8b0bee51-dd16-47a2-9247-23f6907eb5c2 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)...