0s autopkgtest [17:54:21]: starting date and time: 2024-11-01 17:54:21+0000
  0s autopkgtest [17:54:21]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [17:54:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fm748eru/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-15@bos03-arm64-17.secgroup --name adt-plucky-arm64-libbio-db-hts-perl-20241101-175420-juju-7f2275-prod-proposed-migration-environment-15-5e7a0627-f71a-4b93-a669-7b507d6a3e48 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/
 87s autopkgtest [17:55:48]: testbed dpkg architecture: arm64
 87s autopkgtest [17:55:48]: testbed apt version: 2.9.8
 87s autopkgtest [17:55:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 88s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [183 kB]
 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 89s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [44.0 kB]
 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2775 kB]
 89s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [241 kB]
 89s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
 89s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2023 kB]
 89s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [36.5 kB]
 90s Fetched 5433 kB in 1s (4062 kB/s)
 90s Reading package lists...
 93s Reading package lists...
 93s Building dependency tree...
 93s Reading state information...
 94s Calculating upgrade...
 95s The following packages will be upgraded:
 95s   libevdev2 libftdi1-2 libinih1 nano python3-lazr.uri
 95s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 95s Need to get 374 kB of archives.
 95s After this operation, 17.4 kB of additional disk space will be used.
 95s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB]
 95s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB]
 96s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB]
 96s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B]
 96s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB]
 96s Fetched 374 kB in 0s (852 kB/s)
 97s (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 ... 79705 files and directories currently installed.)
 97s Preparing to unpack .../libevdev2_1.13.3+dfsg-1_arm64.deb ...
 97s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ...
 97s Preparing to unpack .../archives/nano_8.2-1_arm64.deb ...
 97s Unpacking nano (8.2-1) over (8.1-1) ...
 97s Preparing to unpack .../libftdi1-2_1.5-7_arm64.deb ...
 97s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ...
 97s Preparing to unpack .../libinih1_58-1ubuntu1_arm64.deb ...
 97s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ...
 97s Preparing to unpack .../python3-lazr.uri_1.0.6-4_all.deb ...
 97s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ...
 97s Setting up libinih1:arm64 (58-1ubuntu1) ...
 97s Setting up python3-lazr.uri (1.0.6-4) ...
 97s Setting up libftdi1-2:arm64 (1.5-7) ...
 97s Setting up nano (8.2-1) ...
 97s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ...
 97s Processing triggers for man-db (2.12.1-3) ...
 98s Processing triggers for install-info (7.1.1-1) ...
 98s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 99s Reading package lists...
 99s Building dependency tree...
 99s Reading state information...
100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
101s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
101s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
101s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
101s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
102s Reading package lists...
102s Reading package lists...
103s Building dependency tree...
103s Reading state information...
103s Calculating upgrade...
104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
104s Reading package lists...
104s Building dependency tree...
104s Reading state information...
105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
108s autopkgtest [17:56:09]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
108s autopkgtest [17:56:09]: @@@@@@@@@@@@@@@@@@@@ apt-source libbio-db-hts-perl
110s Get:1 http://ftpmaster.internal/ubuntu plucky/universe libbio-db-hts-perl 3.01-4build4 (dsc) [2270 B]
110s Get:2 http://ftpmaster.internal/ubuntu plucky/universe libbio-db-hts-perl 3.01-4build4 (tar) [5251 kB]
110s Get:3 http://ftpmaster.internal/ubuntu plucky/universe libbio-db-hts-perl 3.01-4build4 (diff) [4060 B]
111s gpgv: Signature made Sun Oct 20 08:30:39 2024 UTC
111s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
111s gpgv: Can't check signature: No public key
111s dpkg-source: warning: cannot verify inline signature for ./libbio-db-hts-perl_3.01-4build4.dsc: no acceptable signature found
111s autopkgtest [17:56:12]: testing package libbio-db-hts-perl version 3.01-4build4
111s autopkgtest [17:56:12]: build not needed
112s autopkgtest [17:56:13]: test autodep8-perl-build-deps: preparing testbed
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
117s Starting pkgProblemResolver with broken count: 0
117s Starting 2 pkgProblemResolver with broken count: 0
117s Done
118s The following additional packages will be installed:
118s   autoconf autodep8 automake autopoint autotools-dev build-essential cpp
118s   cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu dctrl-tools debhelper
118s   debugedit dh-autoreconf dh-strip-nondeterminism dwz g++ g++-14
118s   g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
118s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian
118s   libarchive-zip-perl libasan8 libbio-db-hts-perl libbio-perl-perl
118s   libbrotli-dev libbz2-dev libcc1-0 libcurl4-gnutls-dev libdata-stag-perl
118s   libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64
118s   libextutils-pkgconfig-perl libfile-stripnondeterminism-perl libgcc-14-dev
118s   libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64
118s   libgnutls28-dev libgomp1 libhts-dev libhts3t64 libhtscodecs2 libhwasan0
118s   libidn2-dev libio-string-perl libisl23 libitm1 liblsan0 liblzma-dev
118s   libmodule-build-perl libmpc3 libnghttp2-dev libp11-kit-dev libpkgconf3
118s   libpsl-dev librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev
118s   libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 libzstd-dev m4
118s   nettle-dev pkg-config pkg-perl-autopkgtest pkgconf pkgconf-bin po-debconf
118s   zlib1g-dev
118s Suggested packages:
118s   autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales
118s   cpp-14-doc debtags dh-make gcc-14-doc gcc-multilib manpages-dev flex bison
118s   gdb gcc-doc gdb-aarch64-linux-gnu gettext-doc libasprintf-dev
118s   libgettextpo-dev bioperl libxml-sax-expatxs-perl libcurl4-doc libidn-dev
118s   libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data
118s   gnutls-bin gnutls-doc liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc
118s   libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
118s   libmail-box-perl
118s Recommended packages:
118s   bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl
118s   libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl
118s   libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
118s   libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl
118s   libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl
118s   libset-scalar-perl libsoap-lite-perl libsort-naturally-perl
118s   libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl
118s   libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl
118s   libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl
118s   libxml-writer-perl libxml-libxml-perl libwww-perl bzip2-doc perl-tk
118s   libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl
118s   libxml-perl libarchive-cpio-perl libmodule-signature-perl libpod-readme-perl
118s   libsoftware-license-perl libtasn1-doc libltdl-dev libmail-sendmail-perl
118s The following NEW packages will be installed:
118s   autoconf autodep8 automake autopkgtest-satdep autopoint autotools-dev
118s   build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
118s   dctrl-tools debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz
118s   g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
118s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian
118s   libarchive-zip-perl libasan8 libbio-db-hts-perl libbio-perl-perl
118s   libbrotli-dev libbz2-dev libcc1-0 libcurl4-gnutls-dev libdata-stag-perl
118s   libdebhelper-perl libdeflate-dev libdeflate0 libevent-2.1-7t64
118s   libextutils-pkgconfig-perl libfile-stripnondeterminism-perl libgcc-14-dev
118s   libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64
118s   libgnutls28-dev libgomp1 libhts-dev libhts3t64 libhtscodecs2 libhwasan0
118s   libidn2-dev libio-string-perl libisl23 libitm1 liblsan0 liblzma-dev
118s   libmodule-build-perl libmpc3 libnghttp2-dev libp11-kit-dev libpkgconf3
118s   libpsl-dev librtmp-dev libssh2-1-dev libssl-dev libstdc++-14-dev
118s   libtasn1-6-dev libtool libtsan2 libubsan1 libunbound8 libzstd-dev m4
118s   nettle-dev pkg-config pkg-perl-autopkgtest pkgconf pkgconf-bin po-debconf
118s   zlib1g-dev
118s 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded.
118s Need to get 83.9 MB/83.9 MB of archives.
118s After this operation, 283 MB of additional disk space will be used.
118s Get:1 /tmp/autopkgtest.qedwvw/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [800 B]
118s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB]
118s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB]
118s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB]
118s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autodep8 all 0.28+nmu1ubuntu1 [13.7 kB]
118s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB]
118s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
118s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB]
118s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
118s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
118s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-7ubuntu1 [10.6 MB]
119s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-7ubuntu1 [1030 B]
119s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B]
119s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB]
119s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-7ubuntu1 [49.7 kB]
119s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB]
119s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-7ubuntu1 [27.8 kB]
119s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-7ubuntu1 [2893 kB]
119s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-7ubuntu1 [1283 kB]
119s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-7ubuntu1 [2691 kB]
119s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-7ubuntu1 [1151 kB]
119s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-7ubuntu1 [1599 kB]
119s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-7ubuntu1 [2594 kB]
119s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-7ubuntu1 [20.9 MB]
119s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-7ubuntu1 [515 kB]
120s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B]
120s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B]
120s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-7ubuntu1 [2474 kB]
120s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-7ubuntu1 [12.1 MB]
120s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-7ubuntu1 [19.8 kB]
120s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B]
120s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B]
120s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
120s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
120s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB]
120s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB]
120s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB]
120s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
120s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B]
120s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB]
120s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB]
120s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB]
120s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
120s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB]
120s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB]
120s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB]
120s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB]
120s Get:48 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB]
120s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-string-perl all 1.08-4 [11.1 kB]
120s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdata-stag-perl all 0.14-3 [372 kB]
120s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbio-perl-perl all 1.7.8-1 [2580 kB]
120s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbio-db-hts-perl arm64 3.01-4build4 [137 kB]
120s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libbrotli-dev arm64 1.1.0-2build2 [360 kB]
120s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB]
120s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10 [140 kB]
120s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libunbound8 arm64 1.20.0-1ubuntu2.1 [431 kB]
120s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls-dane0t64 arm64 3.8.6-2ubuntu1 [24.0 kB]
120s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls-openssl27t64 arm64 3.8.6-2ubuntu1 [24.0 kB]
120s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libidn2-dev arm64 2.3.7-2build2 [120 kB]
120s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit-dev arm64 0.25.5-2ubuntu1 [22.7 kB]
120s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libtasn1-6-dev arm64 4.19.0-3build1 [90.6 kB]
120s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2ubuntu7 [10.1 kB]
120s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2ubuntu7 [335 kB]
120s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 nettle-dev arm64 3.10-1 [1189 kB]
120s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls28-dev arm64 3.8.6-2ubuntu1 [1132 kB]
120s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-3ubuntu1 [31.5 kB]
120s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-3ubuntu1 [20.9 kB]
120s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-3ubuntu1 [16.8 kB]
120s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libnghttp2-dev arm64 1.62.1-2 [120 kB]
120s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpsl-dev arm64 0.21.2-1.1build1 [77.2 kB]
120s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
120s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2build7 [69.4 kB]
120s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libssl-dev arm64 3.3.1-2ubuntu2 [3176 kB]
121s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libssh2-1-dev arm64 1.11.0-7 [264 kB]
121s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libzstd-dev arm64 1.5.6+dfsg-1 [352 kB]
121s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl4-gnutls-dev arm64 8.9.1-2ubuntu2 [485 kB]
121s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.21-1 [53.8 kB]
121s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 pkg-config arm64 1.8.1-3ubuntu1 [7402 B]
121s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 libextutils-pkgconfig-perl all 1.16-3 [8524 B]
121s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.2-2 [179 kB]
121s Get:81 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts-dev arm64 1.20+ds-2 [5918 kB]
121s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmodule-build-perl all 0.423400-2 [200 kB]
121s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-perl-autopkgtest all 0.79 [18.5 kB]
121s Fetched 83.9 MB in 3s (27.1 MB/s)
121s Selecting previously unselected package m4.
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121s Preparing to unpack .../00-m4_1.4.19-4build1_arm64.deb ...
121s Unpacking m4 (1.4.19-4build1) ...
121s Selecting previously unselected package autoconf.
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121s Selecting previously unselected package dctrl-tools.
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121s Selecting previously unselected package autodep8.
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122s Selecting previously unselected package autotools-dev.
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122s Selecting previously unselected package autopoint.
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122s Selecting previously unselected package libisl23:arm64.
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122s Selecting previously unselected package libmpc3:arm64.
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122s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
122s Preparing to unpack .../09-cpp-14-aarch64-linux-gnu_14.2.0-7ubuntu1_arm64.deb ...
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122s Selecting previously unselected package libcc1-0:arm64.
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122s Selecting previously unselected package libgomp1:arm64.
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122s Selecting previously unselected package libasan8:arm64.
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123s Selecting previously unselected package libubsan1:arm64.
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123s Selecting previously unselected package libstdc++-14-dev:arm64.
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124s Selecting previously unselected package g++-14-aarch64-linux-gnu.
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124s Unpacking g++-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ...
124s Selecting previously unselected package g++-14.
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124s Unpacking g++-14 (14.2.0-7ubuntu1) ...
124s Selecting previously unselected package g++-aarch64-linux-gnu.
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124s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
124s Selecting previously unselected package g++.
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124s Unpacking g++ (4:14.1.0-2ubuntu1) ...
124s Selecting previously unselected package build-essential.
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124s Selecting previously unselected package libdebhelper-perl.
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124s Selecting previously unselected package libtool.
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124s Selecting previously unselected package libarchive-zip-perl.
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124s Selecting previously unselected package libfile-stripnondeterminism-perl.
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124s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
124s Selecting previously unselected package dh-strip-nondeterminism.
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124s Unpacking dh-strip-nondeterminism (1.14.0-1) ...
124s Selecting previously unselected package debugedit.
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125s Unpacking intltool-debian (0.35.0+20060710.6) ...
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125s Selecting previously unselected package libdeflate0:arm64.
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125s Unpacking libdeflate0:arm64 (1.21-1) ...
125s Selecting previously unselected package libhtscodecs2:arm64.
125s Preparing to unpack .../45-libhtscodecs2_1.6.0-1build1_arm64.deb ...
125s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ...
125s Selecting previously unselected package libhts3t64:arm64.
125s Preparing to unpack .../46-libhts3t64_1.20+ds-2_arm64.deb ...
125s Unpacking libhts3t64:arm64 (1.20+ds-2) ...
125s Selecting previously unselected package libio-string-perl.
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125s Selecting previously unselected package libdata-stag-perl.
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125s Selecting previously unselected package libbio-perl-perl.
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125s Selecting previously unselected package libbio-db-hts-perl.
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125s Unpacking libbio-db-hts-perl (3.01-4build4) ...
125s Selecting previously unselected package libbrotli-dev:arm64.
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125s Unpacking libbrotli-dev:arm64 (1.1.0-2build2) ...
125s Selecting previously unselected package libbz2-dev:arm64.
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125s Unpacking libbz2-dev:arm64 (1.0.8-6) ...
125s Selecting previously unselected package libevent-2.1-7t64:arm64.
125s Preparing to unpack .../53-libevent-2.1-7t64_2.1.12-stable-10_arm64.deb ...
125s Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10) ...
125s Selecting previously unselected package libunbound8:arm64.
125s Preparing to unpack .../54-libunbound8_1.20.0-1ubuntu2.1_arm64.deb ...
125s Unpacking libunbound8:arm64 (1.20.0-1ubuntu2.1) ...
125s Selecting previously unselected package libgnutls-dane0t64:arm64.
125s Preparing to unpack .../55-libgnutls-dane0t64_3.8.6-2ubuntu1_arm64.deb ...
125s Unpacking libgnutls-dane0t64:arm64 (3.8.6-2ubuntu1) ...
125s Selecting previously unselected package libgnutls-openssl27t64:arm64.
125s Preparing to unpack .../56-libgnutls-openssl27t64_3.8.6-2ubuntu1_arm64.deb ...
125s Unpacking libgnutls-openssl27t64:arm64 (3.8.6-2ubuntu1) ...
125s Selecting previously unselected package libidn2-dev:arm64.
126s Preparing to unpack .../57-libidn2-dev_2.3.7-2build2_arm64.deb ...
126s Unpacking libidn2-dev:arm64 (2.3.7-2build2) ...
126s Selecting previously unselected package libp11-kit-dev:arm64.
126s Preparing to unpack .../58-libp11-kit-dev_0.25.5-2ubuntu1_arm64.deb ...
126s Unpacking libp11-kit-dev:arm64 (0.25.5-2ubuntu1) ...
126s Selecting previously unselected package libtasn1-6-dev:arm64.
126s Preparing to unpack .../59-libtasn1-6-dev_4.19.0-3build1_arm64.deb ...
126s Unpacking libtasn1-6-dev:arm64 (4.19.0-3build1) ...
126s Selecting previously unselected package libgmpxx4ldbl:arm64.
126s Preparing to unpack .../60-libgmpxx4ldbl_2%3a6.3.0+dfsg-2ubuntu7_arm64.deb ...
126s Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2ubuntu7) ...
126s Selecting previously unselected package libgmp-dev:arm64.
126s Preparing to unpack .../61-libgmp-dev_2%3a6.3.0+dfsg-2ubuntu7_arm64.deb ...
126s Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-2ubuntu7) ...
126s Selecting previously unselected package nettle-dev:arm64.
126s Preparing to unpack .../62-nettle-dev_3.10-1_arm64.deb ...
126s Unpacking nettle-dev:arm64 (3.10-1) ...
126s Selecting previously unselected package libgnutls28-dev:arm64.
126s Preparing to unpack .../63-libgnutls28-dev_3.8.6-2ubuntu1_arm64.deb ...
126s Unpacking libgnutls28-dev:arm64 (3.8.6-2ubuntu1) ...
126s Selecting previously unselected package libpkgconf3:arm64.
126s Preparing to unpack .../64-libpkgconf3_1.8.1-3ubuntu1_arm64.deb ...
126s Unpacking libpkgconf3:arm64 (1.8.1-3ubuntu1) ...
126s Selecting previously unselected package pkgconf-bin.
126s Preparing to unpack .../65-pkgconf-bin_1.8.1-3ubuntu1_arm64.deb ...
126s Unpacking pkgconf-bin (1.8.1-3ubuntu1) ...
126s Selecting previously unselected package pkgconf:arm64.
126s Preparing to unpack .../66-pkgconf_1.8.1-3ubuntu1_arm64.deb ...
126s Unpacking pkgconf:arm64 (1.8.1-3ubuntu1) ...
126s Selecting previously unselected package libnghttp2-dev:arm64.
126s Preparing to unpack .../67-libnghttp2-dev_1.62.1-2_arm64.deb ...
126s Unpacking libnghttp2-dev:arm64 (1.62.1-2) ...
126s Selecting previously unselected package libpsl-dev:arm64.
126s Preparing to unpack .../68-libpsl-dev_0.21.2-1.1build1_arm64.deb ...
126s Unpacking libpsl-dev:arm64 (0.21.2-1.1build1) ...
126s Selecting previously unselected package zlib1g-dev:arm64.
126s Preparing to unpack .../69-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ...
126s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
126s Selecting previously unselected package librtmp-dev:arm64.
126s Preparing to unpack .../70-librtmp-dev_2.4+20151223.gitfa8646d.1-2build7_arm64.deb ...
126s Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2build7) ...
126s Selecting previously unselected package libssl-dev:arm64.
126s Preparing to unpack .../71-libssl-dev_3.3.1-2ubuntu2_arm64.deb ...
126s Unpacking libssl-dev:arm64 (3.3.1-2ubuntu2) ...
126s Selecting previously unselected package libssh2-1-dev:arm64.
126s Preparing to unpack .../72-libssh2-1-dev_1.11.0-7_arm64.deb ...
126s Unpacking libssh2-1-dev:arm64 (1.11.0-7) ...
126s Selecting previously unselected package libzstd-dev:arm64.
126s Preparing to unpack .../73-libzstd-dev_1.5.6+dfsg-1_arm64.deb ...
126s Unpacking libzstd-dev:arm64 (1.5.6+dfsg-1) ...
126s Selecting previously unselected package libcurl4-gnutls-dev:arm64.
127s Preparing to unpack .../74-libcurl4-gnutls-dev_8.9.1-2ubuntu2_arm64.deb ...
127s Unpacking libcurl4-gnutls-dev:arm64 (8.9.1-2ubuntu2) ...
127s Selecting previously unselected package libdeflate-dev:arm64.
127s Preparing to unpack .../75-libdeflate-dev_1.21-1_arm64.deb ...
127s Unpacking libdeflate-dev:arm64 (1.21-1) ...
127s Selecting previously unselected package pkg-config:arm64.
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127s Unpacking pkg-config:arm64 (1.8.1-3ubuntu1) ...
127s Selecting previously unselected package libextutils-pkgconfig-perl.
127s Preparing to unpack .../77-libextutils-pkgconfig-perl_1.16-3_all.deb ...
127s Unpacking libextutils-pkgconfig-perl (1.16-3) ...
127s Selecting previously unselected package liblzma-dev:arm64.
127s Preparing to unpack .../78-liblzma-dev_5.6.2-2_arm64.deb ...
127s Unpacking liblzma-dev:arm64 (5.6.2-2) ...
127s Selecting previously unselected package libhts-dev:arm64.
127s Preparing to unpack .../79-libhts-dev_1.20+ds-2_arm64.deb ...
127s Unpacking libhts-dev:arm64 (1.20+ds-2) ...
127s Selecting previously unselected package libmodule-build-perl.
127s Preparing to unpack .../80-libmodule-build-perl_0.423400-2_all.deb ...
127s Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl'
127s 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'
127s Unpacking libmodule-build-perl (0.423400-2) ...
127s Selecting previously unselected package pkg-perl-autopkgtest.
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127s Unpacking pkg-perl-autopkgtest (0.79) ...
127s Selecting previously unselected package autopkgtest-satdep.
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127s Unpacking autopkgtest-satdep (0) ...
127s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ...
127s Setting up libgnutls-openssl27t64:arm64 (3.8.6-2ubuntu1) ...
127s Setting up libzstd-dev:arm64 (1.5.6+dfsg-1) ...
127s Setting up libarchive-zip-perl (1.68-1) ...
127s Setting up libdebhelper-perl (13.20ubuntu1) ...
127s Setting up libdeflate0:arm64 (1.21-1) ...
127s Setting up m4 (1.4.19-4build1) ...
127s Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10) ...
127s Setting up libgomp1:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libpsl-dev:arm64 (0.21.2-1.1build1) ...
127s Setting up libmodule-build-perl (0.423400-2) ...
127s Setting up libio-string-perl (1.08-4) ...
127s Setting up autotools-dev (20220109.1) ...
127s Setting up libunbound8:arm64 (1.20.0-1ubuntu2.1) ...
127s Setting up libpkgconf3:arm64 (1.8.1-3ubuntu1) ...
127s Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2ubuntu7) ...
127s Setting up libgnutls-dane0t64:arm64 (3.8.6-2ubuntu1) ...
127s Setting up libssl-dev:arm64 (3.3.1-2ubuntu2) ...
127s Setting up libmpc3:arm64 (1.3.1-1build2) ...
127s Setting up autopoint (0.22.5-2) ...
127s Setting up pkgconf-bin (1.8.1-3ubuntu1) ...
127s Setting up libidn2-dev:arm64 (2.3.7-2build2) ...
127s Setting up autoconf (2.72-3) ...
127s Setting up liblzma-dev:arm64 (5.6.2-2) ...
127s Setting up libubsan1:arm64 (14.2.0-7ubuntu1) ...
127s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
127s Setting up dwz (0.15-1build6) ...
127s Setting up libdata-stag-perl (0.14-3) ...
127s Setting up libhwasan0:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libasan8:arm64 (14.2.0-7ubuntu1) ...
127s Setting up debugedit (1:5.1-1) ...
127s Setting up libhts3t64:arm64 (1.20+ds-2) ...
127s Setting up libbio-perl-perl (1.7.8-1) ...
127s Setting up libtsan2:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libisl23:arm64 (0.27-1) ...
127s Setting up libtasn1-6-dev:arm64 (4.19.0-3build1) ...
127s Setting up libdeflate-dev:arm64 (1.21-1) ...
127s Setting up libcc1-0:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libbrotli-dev:arm64 (1.1.0-2build2) ...
127s Setting up liblsan0:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libp11-kit-dev:arm64 (0.25.5-2ubuntu1) ...
127s Setting up dctrl-tools (2.24-3build3) ...
127s Setting up libitm1:arm64 (14.2.0-7ubuntu1) ...
127s Setting up autodep8 (0.28+nmu1ubuntu1) ...
127s Setting up libbz2-dev:arm64 (1.0.8-6) ...
127s Setting up automake (1:1.16.5-1.3ubuntu1) ...
127s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
127s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
127s Setting up gettext (0.22.5-2) ...
127s Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-2ubuntu7) ...
127s Setting up nettle-dev:arm64 (3.10-1) ...
127s Setting up libbio-db-hts-perl (3.01-4build4) ...
127s Setting up pkgconf:arm64 (1.8.1-3ubuntu1) ...
127s Setting up intltool-debian (0.35.0+20060710.6) ...
127s Setting up pkg-config:arm64 (1.8.1-3ubuntu1) ...
127s Setting up libssh2-1-dev:arm64 (1.11.0-7) ...
127s Setting up pkg-perl-autopkgtest (0.79) ...
127s Setting up dh-strip-nondeterminism (1.14.0-1) ...
127s Setting up cpp-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ...
127s Setting up libgcc-14-dev:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libstdc++-14-dev:arm64 (14.2.0-7ubuntu1) ...
127s Setting up libgnutls28-dev:arm64 (3.8.6-2ubuntu1) ...
127s Setting up libnghttp2-dev:arm64 (1.62.1-2) ...
127s Setting up libextutils-pkgconfig-perl (1.16-3) ...
127s Setting up po-debconf (1.0.21+nmu1) ...
127s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
127s Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2build7) ...
127s Setting up cpp-14 (14.2.0-7ubuntu1) ...
127s Setting up cpp (4:14.1.0-2ubuntu1) ...
127s Setting up gcc-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ...
127s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
127s Setting up g++-14-aarch64-linux-gnu (14.2.0-7ubuntu1) ...
127s Setting up libcurl4-gnutls-dev:arm64 (8.9.1-2ubuntu2) ...
127s Setting up gcc-14 (14.2.0-7ubuntu1) ...
127s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
127s Setting up g++-14 (14.2.0-7ubuntu1) ...
127s Setting up libtool (2.4.7-7build1) ...
127s Setting up libhts-dev:arm64 (1.20+ds-2) ...
127s Setting up gcc (4:14.1.0-2ubuntu1) ...
127s Setting up dh-autoreconf (20) ...
127s Setting up g++ (4:14.1.0-2ubuntu1) ...
127s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
127s Setting up build-essential (12.10ubuntu1) ...
127s Setting up debhelper (13.20ubuntu1) ...
127s Setting up autopkgtest-satdep (0) ...
127s Processing triggers for man-db (2.12.1-3) ...
129s Processing triggers for install-info (7.1.1-1) ...
130s Processing triggers for libc-bin (2.40-1ubuntu3) ...
134s (Reading database ... 84298 files and directories currently installed.)
134s Removing autopkgtest-satdep (0) ...
134s autopkgtest [17:56:35]: test autodep8-perl-build-deps: /usr/share/pkg-perl-autopkgtest/runner build-deps
134s autopkgtest [17:56:35]: test autodep8-perl-build-deps: [-----------------------
135s t/00load.t ....... 
135s ok 1 - use Bio::DB::HTS;
135s ok 2 - use Bio::DB::HTS::Tabix;
135s ok 3 - use Bio::DB::HTS::Tabix::Iterator;
135s ok 4 - use Bio::DB::HTS::Kseq;
135s 1..4
135s ok
136s t/01bam.t ........ 
136s 1..452
136s # Running under perl version 5.040000 for linux
136s # Current time local: Fri Nov  1 17:56:36 2024
136s # Current time GMT:   Fri Nov  1 17:56:36 2024
136s # Using Test.pm version 1.31
136s ok 1
136s ok 2
136s ok 3
136s ok 4
136s ok 5
136s ok 6
136s ok 7
136s ok 8
136s ok 9
136s ok 10
136s ok 11
136s ok 12
136s ok 13
136s ok 14
136s ok 15
136s ok 16
136s ok 17
136s ok 18
136s ok 19
136s ok 20
136s ok 21
136s ok 22
136s ok 23
136s ok 24
136s ok 25
136s ok 26
136s ok 27
136s ok 28
136s ok 29
136s ok 30
136s ok 31
136s ok 32
136s ok 33
136s ok 34
136s ok 35
136s ok 36
136s ok 37
136s ok 38
136s ok 39
136s ok 40
136s ok 41
136s ok 42
136s ok 43
136s ok 44
136s ok 45
136s ok 46
136s ok 47
136s ok 48
136s ok 49
136s ok 50
136s ok 51
136s ok 52
136s ok 53
136s ok 54
136s ok 55
136s ok 56
136s ok 57
136s ok 58
136s ok 59
136s ok 60
136s ok 61
136s ok 62
136s ok 63
136s ok 64
136s ok 65
136s ok 66
136s ok 67
136s ok 68
136s ok 69
136s ok 70
136s ok 71
136s ok 72
136s ok 73
136s ok 74
136s ok 75
136s ok 76
136s ok 77
136s ok 78
136s ok 79
136s ok 80
136s ok 81
136s ok 82
136s ok 83
136s ok 84
136s ok 85
136s ok 86
136s ok 87
136s ok 88
136s ok 89
136s ok 90
136s ok 91
136s ok 92
136s ok 93
136s ok 94
136s ok 95
136s ok 96
136s ok 97
136s ok 98
136s ok 99
136s ok 100
136s ok 101
136s ok 102
136s ok 103
136s ok 104
136s ok 105
136s ok 106
136s ok 107
136s ok 108
136s ok 109
136s ok 110
136s ok 111
136s ok 112
136s ok 113
136s ok 114
136s ok 115
136s ok 116
136s ok 117
136s ok 118
136s ok 119
136s ok 120
136s ok 121
136s ok 122
136s ok 123
136s ok 124
136s ok 125
136s ok 126
136s ok 127
136s ok 128
136s ok 129
136s ok 130
136s ok 131
136s ok 132
136s ok 133
136s ok 134
136s ok 135
136s ok 136
136s ok 137
136s ok 138
136s ok 139
136s ok 140
136s ok 141
136s ok 142
136s ok 143
136s ok 144
136s ok 145
136s ok 146
136s ok 147
136s ok 148
136s ok 149
136s ok 150
136s ok 151
136s ok 152
136s ok 153
136s ok 154
136s ok 155
136s ok 156
136s ok 157
136s ok 158
136s ok 159
136s ok 160
136s ok 161
136s ok 162
136s ok 163
136s ok 164
136s ok 165
136s ok 166
136s ok 167
136s ok 168
136s ok 169
136s ok 170
136s ok 171
136s ok 172
136s ok 173
136s ok 174
136s ok 175
136s ok 176
136s ok 177
136s ok 178
136s ok 179
136s ok 180
136s ok 181
136s ok 182
136s ok 183
136s ok 184
136s ok 185
136s ok 186
136s ok 187
136s ok 188
136s ok 189
136s ok 190
136s ok 191
136s ok 192
136s ok 193
136s ok 194
136s ok 195
136s ok 196
136s ok 197
136s ok 198
136s ok 199
136s ok 200
136s ok 201
136s ok 202
136s ok 203
136s ok 204
136s ok 205
136s ok 206
136s ok 207
136s ok 208
136s ok 209
136s ok 210
136s ok 211
136s ok 212
136s ok 213
136s ok 214
136s ok 215
136s ok 216
136s ok 217
136s ok 218
136s ok 219
136s ok 220
136s ok 221
136s ok 222
136s ok 223
136s ok 224
136s ok 225
136s ok 226
136s ok 227
136s ok 228
136s ok 229
136s ok 230
136s ok 231
136s ok 232
136s ok 233
136s ok 234
136s ok 235
136s ok 236
136s ok 237
136s ok 238
136s ok 239
136s ok 240
136s ok 241
136s ok 242
136s ok 243
136s ok 244
136s ok 245
136s ok 246
136s ok 247
136s ok 248
136s ok 249
136s ok 250
136s ok 251
136s ok 252
136s ok 253
136s ok 254
136s ok 255
136s ok 256
136s ok 257
136s ok 258
136s ok 259
136s ok 260
136s ok 261
136s ok 262
136s ok 263
136s ok 264
136s ok 265
136s ok 266
136s ok 267
136s ok 268
136s ok 269
136s ok 270
136s ok 271
136s ok 272
136s ok 273
136s ok 274
136s ok 275
136s ok 276
136s ok 277
136s ok 278
136s ok 279
136s ok 280
136s ok 281
136s ok 282
136s ok 283
136s ok 284
136s ok 285
136s ok 286
136s ok 287
136s ok 288
136s ok 289
136s ok 290
136s ok 291
136s ok 292
136s ok 293
136s ok 294
136s ok 295
136s ok 296
136s ok 297
136s ok 298
136s ok 299
136s ok 300
136s ok 301
136s ok 302
136s ok 303
136s ok 304
136s ok 305
136s ok 306
136s ok 307
136s ok 308
136s ok 309
136s ok 310
136s ok 311
136s ok 312
136s ok 313
136s ok 314
136s ok 315
136s ok 316
136s ok 317
136s ok 318
136s ok 319
136s ok 320
136s ok 321
136s ok 322
136s ok 323
136s ok 324
136s ok 325
136s ok 326
136s ok 327
136s ok 328
136s ok 329
136s ok 330
136s ok 331
136s ok 332
136s ok 333
136s ok 334
136s ok 335
136s ok 336
136s ok 337
136s ok 338
136s ok 339
136s ok 340
136s ok 341
136s ok 342
136s ok 343
136s ok 344
136s ok 345
136s ok 346
136s ok 347
136s ok 348
136s ok 349
136s ok 350
136s ok 351
136s ok 352
136s ok 353
136s ok 354
136s ok 355
136s ok 356
136s ok 357
136s ok 358
136s ok 359
136s ok 360
136s ok 361
136s ok 362
136s ok 363
136s ok 364
136s ok 365
136s ok 366
136s ok 367
136s ok 368
136s ok 369
136s ok 370
136s ok 371
136s ok 372
136s ok 373
136s ok 374
136s ok 375
136s ok 376
136s ok 377
136s ok 378
136s ok 379
136s ok 380
136s ok 381
136s ok 382
136s ok 383
136s ok 384
136s ok 385
136s ok 386
136s ok 387
136s ok 388
136s ok 389
136s ok 390
136s ok 391
136s ok 392
136s ok 393
136s ok 394
136s ok 395
136s ok 396
136s ok 397
136s ok 398
136s ok 399
136s ok 400
136s ok 401
136s ok 402
136s ok 403
136s ok 404
136s ok 405
136s ok 406
136s ok 407
136s ok 408
136s ok 409
136s ok 410
136s ok 411
136s ok 412
136s ok 413
136s ok 414
136s ok 415
136s ok 416
136s ok 417
136s ok 418
136s ok 419
136s ok 420
136s ok 421
136s ok 422
136s ok 423
136s ok 424
136s ok 425
136s ok 426
136s ok 427
136s ok 428
136s ok 429
136s ok 430
136s ok 431
136s ok 432
136s ok 433
136s ok 434
136s ok 435
136s ok 436
136s ok 437
136s ok 438
136s ok 439
136s ok 440
136s ok 441
136s ok 442
136s ok 443
136s ok 444
136s ok 445
136s ok 446
136s ok 447
136s ok 448
136s ok 449
136s ok 450
136s ok 451
136s ok 452
136s ok
136s t/02faidx.t ...... 
136s 1..15
136s ok 1 - use Bio::DB::HTS;
136s ok 2 - use Bio::DB::HTS::Faidx;
136s ok 3
136s ok 4
136s ok 5
136s ok 6
136s ok 7
136s ok 8
136s ok 9
136s ok 10
136s ok 11
136s ok 12
136s # 230218
136s ok 13 - length of I
136s ok 14 - has sequence I
136s ok 15 - Does not have sequence II
136s ok
140s t/03cram.t ....... 
140s 1..139
140s # Running under perl version 5.040000 for linux
140s # Current time local: Fri Nov  1 17:56:37 2024
140s # Current time GMT:   Fri Nov  1 17:56:37 2024
140s # Using Test.pm version 1.31
140s ok 1
140s ok 2
140s ok 3
140s ok 4
140s ok 5
140s ok 6
140s ok 7
140s ok 8
140s ok 9
140s ok 10
140s ok 11
140s ok 12
140s ok 13
140s ok 14
140s ok 15
140s ok 16
140s ok 17
140s ok 18
140s ok 19
140s ok 20
140s ok 21
140s ok 22
140s ok 23
140s ok 24
140s ok 25
140s ok 26
140s ok 27
140s ok 28
140s ok 29
140s ok 30
140s ok 31
140s ok 32
140s ok 33
140s ok 34
140s ok 35
140s ok 36
140s ok 37
140s ok 38
140s ok 39
140s ok 40
140s ok 41
140s ok 42
140s ok 43
140s ok 44
140s ok 45
140s ok 46
140s ok 47
140s ok 48
140s ok 49
140s ok 50
140s ok 51
140s ok 52
140s ok 53
140s ok 54
140s ok 55
140s ok 56
140s ok 57
140s ok 58
140s ok 59
140s ok 60
140s ok 61
140s ok 62
140s ok 63
140s ok 64
140s ok 65
140s ok 66
140s ok 67
140s ok 68
140s ok 69
140s ok 70
140s ok 71
140s ok 72
140s ok 73
140s ok 74
140s ok 75
140s ok 76
140s ok 77
140s ok 78
140s ok 79
140s ok 80
140s ok 81
140s ok 82
140s ok 83
140s ok 84
140s ok 85
140s ok 86
140s ok 87
140s ok 88
140s ok 89
140s ok 90
140s ok 91
140s ok 92
140s ok 93
140s ok 94
140s ok 95
140s ok 96
140s ok 97
140s ok 98
140s ok 99
140s ok 100
140s ok 101
140s ok 102
140s ok 103
140s ok 104
140s ok 105
140s ok 106
140s ok 107
140s ok 108
140s ok 109
140s ok 110
140s ok 111
140s ok 112
140s ok 113
140s ok 114
140s ok 115
140s ok 116
140s ok 117
140s ok 118
140s ok 119
140s ok 120
140s ok 121
140s ok 122
140s ok 123
140s ok 124
140s ok 125
140s ok 126
140s ok 127
140s ok 128
140s ok 129
140s ok 130
140s ok 131
140s ok 132
140s ok 133
140s ok 134
140s ok 135
140s ok 136
140s ok 137
140s ok 138
140s ok 139
140s ok
140s t/04tabix.t ...... 
140s 1..21
140s ok 1 - use Bio::DB::HTS::Tabix;
140s ok 2 - \#CHROM  FROM    TO      GERP
140s ok 3 - \#CHROM  FROM    TO      GERP
140s ok 4 - can query a region
140s ok 5 - can get a value from the iterator
140s ok 6 - row value is correct
140s ok 7 - correct number of values come back from the iterator
140s ok 8 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 9 - seqnames are correct
140s ok 10 - can query a region with ':' in chr
140s ok 11 - can get a value from the iterator
140s ok 12 - row value is correct with ':' in chr
140s ok 13 - can query a region with ':' in chr, no end
140s ok 14 - can get a value from the iterator
140s ok 15 - row value is correct with ':' in chr, no end
140s ok 16 - can query a region with ':' in chr, no coord
140s ok 17 - can get a value from the iterator
140s ok 18 - row value is correct with ':' in chr, no coord
140s ok 19 - querying non existent chrom
140s ok 20 - \#\#fileformat=VCFv4.2
140s ok 21 - \#\#reference=human_b36_both.fasta
140s ok
140s t/05vcf.t ........ 
140s 1..177
140s ok 1 - use Bio::DB::HTS::VCF;
140s ok 2 - use Bio::DB::HTS::VCF::Row;
140s ok 3 - use Bio::DB::HTS::VCF::RowPtr;
140s ok 4 - use Bio::DB::HTS::VCF::Header;
140s ok 5 - use Bio::DB::HTS::VCF::HeaderPtr;
140s ok 6 - Chromosome value read
140s ok 7 - Chromosome value read
140s ok 8 - Position value read
140s ok 9 - Quality value read
140s ok 10 - Quality value read
140s ok 11 - ID value read
140s ok 12 - Number of alleles value read
140s ok 13 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 14 - alleles are correct
140s ok 15 - VCF file open
140s ok 16 - correct number of variants identified in file
140s ok 17 - Header formatted string
140s ok 18 - VCF Header version matches
140s ok 19 - Number of samples
140s ok 20 - sample names correct
140s ok 21 - Number of seqnames
140s ok 22
140s ok 23 - sequence names correct
140s ok 24 - Next row
140s ok 25 - Chromosome value read
140s ok 26 - Position value read
140s ok 27 - ID value read
140s ok 28 - Num Filters OK
140s ok 29 - Actual Filter present
140s ok 30 - PASS filter absent
140s ok 31 - Variant type matches
140s ok 32 - info read correctly
140s ok 33 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 34 - info flag read correctly
140s ok 35 - info flag type correct
140s ok 36 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 37 - info float read correctly
140s ok 38 - info float type correct
140s ok 39 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 40 - info string read correctly
140s ok 41 - info String type correct
140s ok 42 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 43 - info ints read correctly
140s ok 44 - info int type correct
140s ok 45 - format int read
140s ok 46 - format int read
140s ok 47 - format id not present
140s ok 48 - format read
140s ok 49 - Next row
140s ok 50 - Chromosome value read
140s ok 51 - Position value read
140s ok 52 - Quality value read
140s ok 53 - Reference value read
140s ok 54 - Num Alleles
140s ok 55 - Is SNP
140s ok 56 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 57 - alleles are correct
140s ok 58 - Num Filters OK
140s ok 59 - PASS Filter present
140s ok 60 - Actual Filter absent
140s ok 61 - Made up filter not existing
140s ok 62 - info read correctly
140s ok 63 - format int read
140s ok 64 - format int read
140s ok 65 - format id not present
140s ok 66 - format read
140s ok 67 - Next row
140s ok 68 - Chromosome value read
140s ok 69 - int format type correct
140s ok 70 - format int read
140s ok 71 - format int read
140s ok 72 - format int read
140s # !!! Not sure this is correct !!!
140s ok 73 - format int read
140s ok 74 - format read
140s ok 75 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 76 - genotypes read correctly
140s ok 77 - format id not found
140s ok 78 - info id not found
140s ok 79 - info read correctly
140s ok 80 - can query a region
140s ok 81 - can get a value from the iterator
140s ok 82 - chr
140s ok 83 - position
140s ok 84 - id
140s ok 85 - reference
140s ok 86 - info
140s ok 87 - info
140s ok 88 - info
140s ok 89 - info
140s ok 90 - can get a value from the iterator
140s ok 91 - chr
140s ok 92 - position
140s ok 93 - id
140s ok 94 - reference
140s ok 95 - info
140s ok 96 - no more results
140s ok 97 - BCF file open
140s ok 98 - correct number of variants identified in file
140s ok 99 - Header formatted string
140s ok 100 - VCF Header version matches
140s ok 101 - Number of samples
140s ok 102 - sample names correct
140s ok 103 - Number of seqnames
140s ok 104 - sequence names correct
140s ok 105 - Next row
140s ok 106 - Chromosome value read
140s ok 107 - Position value read
140s ok 108 - ID value read
140s ok 109 - Num Filters OK
140s ok 110 - Actual Filter present
140s ok 111 - PASS filter absent
140s ok 112 - Variant type matches
140s ok 113 - info read correctly
140s ok 114 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 115 - info flag read correctly
140s ok 116 - info flag type correct
140s ok 117 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 118 - info float read correctly
140s ok 119 - info float type correct
140s ok 120 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 121 - info string read correctly
140s ok 122 - info String type correct
140s ok 123 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 124 - info ints read correctly
140s ok 125 - info int type correct
140s ok 126 - format int read
140s ok 127 - format int read
140s ok 128 - format ID not present
140s ok 129 - format read
140s ok 130 - Next row
140s ok 131 - Chromosome value read
140s ok 132 - Position value read
140s ok 133 - Quality value read
140s ok 134 - Reference value read
140s ok 135 - Num Alleles
140s ok 136 - Is SNP
140s ok 137 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 138 - alleles are correct
140s ok 139 - Num Filters OK
140s ok 140 - PASS Filter present
140s ok 141 - Actual Filter absent
140s ok 142 - Made up filter not existing
140s ok 143 - info read correctly
140s ok 144 - format int read
140s ok 145 - format int read
140s ok 146 - format ID not present
140s ok 147 - format read
140s ok 148 - Next row
140s ok 149 - Chromosome value read
140s ok 150 - int format type correct
140s ok 151 - format int read
140s ok 152 - format int read
140s ok 153 - format int read
140s # !!! Not sure this is correct !!!
140s ok 154 - format int read
140s ok 155 - format read
140s ok 156 - A reference of type 'ARRAY' isa 'ARRAY'
140s ok 157 - genotypes read correctly
140s ok 158 - format id not found
140s ok 159 - info id not found
140s ok 160 - info read correctly
140s ok 161 - can query a region
140s ok 162 - can get a value from the iterator
140s ok 163 - chr
140s ok 164 - position
140s ok 165 - id
140s ok 166 - reference
140s ok 167 - info
140s ok 168 - info
140s ok 169 - info
140s ok 170 - info
140s ok 171 - can get a value from the iterator
140s ok 172 - chr
140s ok 173 - position
140s ok 174 - id
140s ok 175 - reference
140s ok 176 - info
140s ok 177 - no more results
140s ok
141s t/06kseq.t ....... 
141s ok 1 - correct num. seqs in bug2335
141s ok 2 - sample sequence obtained
141s ok 3 - seq matches bug2335
141s ok 4 - desc matches bug2335
141s ok 5 - name matches bug2335
141s ok 6 - qual matches bug2335
141s ok 7 - Checking qual and seq lengths are the same in bug2335
141s ok 8 - Checking qual and seq lengths are the same using object methods in bug2335
141s ok 9 - correct num. seqs in evil_wrapping
141s ok 10 - sample sequence obtained
141s ok 11 - seq matches evil_wrapping
141s ok 12 - desc matches evil_wrapping
141s ok 13 - name matches evil_wrapping
141s ok 14 - qual matches evil_wrapping
141s ok 15 - Checking qual and seq lengths are the same in evil_wrapping
141s ok 16 - Checking qual and seq lengths are the same using object methods in evil_wrapping
141s ok 17 - correct num. seqs in example
141s ok 18 - sample sequence obtained
141s ok 19 - seq matches example
141s ok 20 - desc matches example
141s ok 21 - name matches example
141s ok 22 - qual matches example
141s ok 23 - Checking qual and seq lengths are the same in example
141s ok 24 - Checking qual and seq lengths are the same using object methods in example
141s ok 25 - correct num. seqs in illumina_faked
141s ok 26 - sample sequence obtained
141s ok 27 - seq matches illumina_faked
141s ok 28 - desc matches illumina_faked
141s ok 29 - name matches illumina_faked
141s ok 30 - qual matches illumina_faked
141s ok 31 - Checking qual and seq lengths are the same in illumina_faked
141s ok 32 - Checking qual and seq lengths are the same using object methods in illumina_faked
141s ok 33 - correct num. seqs in sanger_93
141s ok 34 - sample sequence obtained
141s ok 35 - seq matches sanger_93
141s ok 36 - desc matches sanger_93
141s ok 37 - name matches sanger_93
141s ok 38 - qual matches sanger_93
141s ok 39 - Checking qual and seq lengths are the same in sanger_93
141s ok 40 - Checking qual and seq lengths are the same using object methods in sanger_93
141s ok 41 - correct num. seqs in sanger_faked
141s ok 42 - sample sequence obtained
141s ok 43 - seq matches sanger_faked
141s ok 44 - desc matches sanger_faked
141s ok 45 - name matches sanger_faked
141s ok 46 - qual matches sanger_faked
141s ok 47 - Checking qual and seq lengths are the same in sanger_faked
141s ok 48 - Checking qual and seq lengths are the same using object methods in sanger_faked
141s ok 49 - correct num. seqs in solexa_example
141s ok 50 - sample sequence obtained
141s ok 51 - seq matches solexa_example
141s ok 52 - desc matches solexa_example
141s ok 53 - name matches solexa_example
141s ok 54 - qual matches solexa_example
141s ok 55 - Checking qual and seq lengths are the same in solexa_example
141s ok 56 - Checking qual and seq lengths are the same using object methods in solexa_example
141s ok 57 - correct num. seqs in solexa_faked
141s ok 58 - sample sequence obtained
141s ok 59 - seq matches solexa_faked
141s ok 60 - desc matches solexa_faked
141s ok 61 - name matches solexa_faked
141s ok 62 - qual matches solexa_faked
141s ok 63 - Checking qual and seq lengths are the same in solexa_faked
141s ok 64 - Checking qual and seq lengths are the same using object methods in solexa_faked
141s ok 65 - correct num. seqs in test1_sanger
141s ok 66 - sample sequence obtained
141s ok 67 - seq matches test1_sanger
141s ok 68 - desc matches test1_sanger
141s ok 69 - name matches test1_sanger
141s ok 70 - qual matches test1_sanger
141s ok 71 - Checking qual and seq lengths are the same in test1_sanger
141s ok 72 - Checking qual and seq lengths are the same using object methods in test1_sanger
141s ok 73 - correct num. seqs in test2_solexa
141s ok 74 - sample sequence obtained
141s ok 75 - seq matches test2_solexa
141s ok 76 - desc matches test2_solexa
141s ok 77 - name matches test2_solexa
141s ok 78 - qual matches test2_solexa
141s ok 79 - Checking qual and seq lengths are the same in test2_solexa
141s ok 80 - Checking qual and seq lengths are the same using object methods in test2_solexa
141s ok 81 - correct num. seqs in test3_illumina
141s ok 82 - sample sequence obtained
141s ok 83 - seq matches test3_illumina
141s ok 84 - desc matches test3_illumina
141s ok 85 - name matches test3_illumina
141s ok 86 - qual matches test3_illumina
141s ok 87 - Checking qual and seq lengths are the same in test3_illumina
141s ok 88 - Checking qual and seq lengths are the same using object methods in test3_illumina
141s ok 89 - correct num. seqs in tricky
141s ok 90 - sample sequence obtained
141s ok 91 - seq matches tricky
141s ok 92 - desc matches tricky
141s ok 93 - name matches tricky
141s ok 94 - qual matches tricky
141s ok 95 - Checking qual and seq lengths are the same in tricky
141s ok 96 - Checking qual and seq lengths are the same using object methods in tricky
141s ok 97 - correct num. seqs in zero_qual
141s ok 98 - sample sequence obtained
141s ok 99 - seq matches zero_qual
141s ok 100 - desc matches zero_qual
141s ok 101 - name matches zero_qual
141s ok 102 - qual matches zero_qual
141s ok 103 - Checking qual and seq lengths are the same in zero_qual
141s ok 104 - Checking qual and seq lengths are the same using object methods in zero_qual
141s 1..104
141s ok
141s t/07cramwrite.t .. 
141s 1..22
141s # Running under perl version 5.040000 for linux
141s # Current time local: Fri Nov  1 17:56:42 2024
141s # Current time GMT:   Fri Nov  1 17:56:42 2024
141s # Using Test.pm version 1.31
141s ok 1
141s ok 2
141s ok 3
141s ok 4
141s ok 5
141s ok 6
141s ok 7
141s ok 8
141s ok 9
141s ok 10
141s ok 11
141s ok 12
141s ok 13
141s ok 14
141s ok 15
141s ok 16
141s ok 17
141s ok 18
141s ok 19
141s ok 20
141s ok 21
141s ok 22
141s ok
142s t/08bamwrite.t ... 
142s 1..22
142s # Running under perl version 5.040000 for linux
142s # Current time local: Fri Nov  1 17:56:42 2024
142s # Current time GMT:   Fri Nov  1 17:56:42 2024
142s # Using Test.pm version 1.31
142s ok 1
142s ok 2
142s ok 3
142s ok 4
142s ok 5
142s ok 6
142s ok 7
142s ok 8
142s ok 9
142s ok 10
142s ok 11
142s ok 12
142s ok 13
142s ok 14
142s ok 15
142s ok 16
142s ok 17
142s ok 18
142s ok 19
142s ok 20
142s ok 21
142s ok 22
142s ok
142s t/09sam.t ........ 
142s ok 1
142s ok 2 # skip Cannot test header reading for htslib < 1.5
142s ok 3 # skip Cannot test header reading for htslib < 1.5
142s ok 4 # skip Cannot test header reading for htslib < 1.5
142s ok 5 # skip Cannot test header reading for htslib < 1.5
142s ok 6 # skip Cannot test header reading for htslib < 1.5
142s ok 7 # skip Cannot test header reading for htslib < 1.5
142s ok 8 # skip Cannot test header reading for htslib < 1.5
142s ok 9 # skip Cannot test header reading for htslib < 1.5
142s ok 10 # skip Cannot test header reading for htslib < 1.5
142s ok 11 # skip Cannot test header reading for htslib < 1.5
142s ok 12
142s ok 13
142s ok 14 # skip Cannot test iterating over alignments for htslib < 1.5
142s ok 15 # skip Cannot test iterating over alignments for htslib < 1.5
142s ok 16 # skip Cannot test iterating over alignments for htslib < 1.5
142s ok 17 # skip Cannot test iterating over alignments for htslib < 1.5
142s ok 18
142s ok 19
142s ok 20
142s ok 21
142s ok 22 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq'
142s ok 23
142s 1..23
142s ok
142s autopkgtest [17:56:43]: test autodep8-perl-build-deps: -----------------------]
142s t/10leak.t ....... skipped: require Test::LeakTrace
142s All tests successful.
142s Files=11, Tests=979,  7 wallclock secs ( 0.09 usr  0.04 sys +  5.61 cusr  0.77 csys =  6.51 CPU)
142s Result: PASS
143s autopkgtest [17:56:44]: test autodep8-perl-build-deps:  - - - - - - - - - - results - - - - - - - - - -
143s autodep8-perl-build-deps PASS
143s autopkgtest [17:56:44]: test autodep8-perl: preparing testbed
222s autopkgtest [17:58:03]: testbed dpkg architecture: arm64
222s autopkgtest [17:58:03]: testbed apt version: 2.9.8
222s autopkgtest [17:58:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup
223s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
223s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [44.0 kB]
223s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
223s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2775 kB]
224s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [183 kB]
224s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [241 kB]
224s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
224s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2023 kB]
224s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [36.5 kB]
224s Fetched 5433 kB in 1s (3951 kB/s)
224s Reading package lists...
227s Reading package lists...
227s Building dependency tree...
227s Reading state information...
228s Calculating upgrade...
228s The following packages will be upgraded:
228s   libevdev2 libftdi1-2 libinih1 nano python3-lazr.uri
228s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
228s Need to get 374 kB of archives.
228s After this operation, 17.4 kB of additional disk space will be used.
228s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB]
229s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB]
229s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB]
229s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B]
229s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB]
229s Fetched 374 kB in 0s (888 kB/s)
230s (Reading database ... 
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(Reading database ... 79705 files and directories currently installed.)
230s Preparing to unpack .../libevdev2_1.13.3+dfsg-1_arm64.deb ...
230s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ...
230s Preparing to unpack .../archives/nano_8.2-1_arm64.deb ...
230s Unpacking nano (8.2-1) over (8.1-1) ...
230s Preparing to unpack .../libftdi1-2_1.5-7_arm64.deb ...
230s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ...
230s Preparing to unpack .../libinih1_58-1ubuntu1_arm64.deb ...
230s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ...
230s Preparing to unpack .../python3-lazr.uri_1.0.6-4_all.deb ...
230s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ...
231s Setting up libinih1:arm64 (58-1ubuntu1) ...
231s Setting up python3-lazr.uri (1.0.6-4) ...
231s Setting up libftdi1-2:arm64 (1.5-7) ...
231s Setting up nano (8.2-1) ...
231s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ...
231s Processing triggers for man-db (2.12.1-3) ...
232s Processing triggers for install-info (7.1.1-1) ...
232s Processing triggers for libc-bin (2.40-1ubuntu3) ...
232s Reading package lists...
232s Building dependency tree...
232s Reading state information...
233s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
233s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
234s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
234s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
234s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
235s Reading package lists...
235s Reading package lists...
235s Building dependency tree...
235s Reading state information...
236s Calculating upgrade...
236s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
236s Reading package lists...
237s Building dependency tree...
237s Reading state information...
237s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
241s Reading package lists...
242s Building dependency tree...
242s Reading state information...
242s Starting pkgProblemResolver with broken count: 0
242s Starting 2 pkgProblemResolver with broken count: 0
242s Done
243s The following additional packages will be installed:
243s   autodep8 dctrl-tools libbio-db-hts-perl libbio-perl-perl libdata-stag-perl
243s   libdeflate0 libhts3t64 libhtscodecs2 libio-string-perl pkg-perl-autopkgtest
243s Suggested packages:
243s   debtags bioperl libxml-sax-expatxs-perl
243s Recommended packages:
243s   bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl
243s   libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl
243s   libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl
243s   libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl
243s   libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl
243s   libset-scalar-perl libsoap-lite-perl libsort-naturally-perl
243s   libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl
243s   libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl
243s   libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl
243s   libxml-writer-perl libxml-libxml-perl libwww-perl perl-tk libgd-gd2-perl
243s   | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl
243s The following NEW packages will be installed:
243s   autodep8 autopkgtest-satdep dctrl-tools libbio-db-hts-perl libbio-perl-perl
243s   libdata-stag-perl libdeflate0 libhts3t64 libhtscodecs2 libio-string-perl
243s   pkg-perl-autopkgtest
243s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded.
243s Need to get 3797 kB/3798 kB of archives.
243s After this operation, 12.2 MB of additional disk space will be used.
243s Get:1 /tmp/autopkgtest.qedwvw/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
243s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB]
244s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 autodep8 all 0.28+nmu1ubuntu1 [13.7 kB]
244s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB]
244s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB]
244s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB]
244s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libio-string-perl all 1.08-4 [11.1 kB]
244s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdata-stag-perl all 0.14-3 [372 kB]
244s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbio-perl-perl all 1.7.8-1 [2580 kB]
244s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libbio-db-hts-perl arm64 3.01-4build4 [137 kB]
244s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-perl-autopkgtest all 0.79 [18.5 kB]
244s Fetched 3797 kB in 1s (5016 kB/s)
245s Selecting previously unselected package dctrl-tools.
245s (Reading database ... 
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(Reading database ... 79705 files and directories currently installed.)
245s Preparing to unpack .../00-dctrl-tools_2.24-3build3_arm64.deb ...
245s Unpacking dctrl-tools (2.24-3build3) ...
245s Selecting previously unselected package autodep8.
245s Preparing to unpack .../01-autodep8_0.28+nmu1ubuntu1_all.deb ...
245s Unpacking autodep8 (0.28+nmu1ubuntu1) ...
245s Selecting previously unselected package libdeflate0:arm64.
245s Preparing to unpack .../02-libdeflate0_1.21-1_arm64.deb ...
245s Unpacking libdeflate0:arm64 (1.21-1) ...
245s Selecting previously unselected package libhtscodecs2:arm64.
245s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_arm64.deb ...
245s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ...
245s Selecting previously unselected package libhts3t64:arm64.
245s Preparing to unpack .../04-libhts3t64_1.20+ds-2_arm64.deb ...
245s Unpacking libhts3t64:arm64 (1.20+ds-2) ...
245s Selecting previously unselected package libio-string-perl.
245s Preparing to unpack .../05-libio-string-perl_1.08-4_all.deb ...
245s Unpacking libio-string-perl (1.08-4) ...
245s Selecting previously unselected package libdata-stag-perl.
245s Preparing to unpack .../06-libdata-stag-perl_0.14-3_all.deb ...
245s Unpacking libdata-stag-perl (0.14-3) ...
245s Selecting previously unselected package libbio-perl-perl.
245s Preparing to unpack .../07-libbio-perl-perl_1.7.8-1_all.deb ...
245s Unpacking libbio-perl-perl (1.7.8-1) ...
245s Selecting previously unselected package libbio-db-hts-perl.
245s Preparing to unpack .../08-libbio-db-hts-perl_3.01-4build4_arm64.deb ...
245s Unpacking libbio-db-hts-perl (3.01-4build4) ...
245s Selecting previously unselected package pkg-perl-autopkgtest.
245s Preparing to unpack .../09-pkg-perl-autopkgtest_0.79_all.deb ...
245s Unpacking pkg-perl-autopkgtest (0.79) ...
245s Selecting previously unselected package autopkgtest-satdep.
245s Preparing to unpack .../10-2-autopkgtest-satdep.deb ...
245s Unpacking autopkgtest-satdep (0) ...
245s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ...
245s Setting up libdeflate0:arm64 (1.21-1) ...
245s Setting up libio-string-perl (1.08-4) ...
245s Setting up libdata-stag-perl (0.14-3) ...
245s Setting up libhts3t64:arm64 (1.20+ds-2) ...
245s Setting up libbio-perl-perl (1.7.8-1) ...
245s Setting up dctrl-tools (2.24-3build3) ...
245s Setting up autodep8 (0.28+nmu1ubuntu1) ...
245s Setting up libbio-db-hts-perl (3.01-4build4) ...
245s Setting up pkg-perl-autopkgtest (0.79) ...
245s Setting up autopkgtest-satdep (0) ...
245s Processing triggers for man-db (2.12.1-3) ...
247s Processing triggers for libc-bin (2.40-1ubuntu3) ...
250s (Reading database ... 81058 files and directories currently installed.)
250s Removing autopkgtest-satdep (0) ...
253s autopkgtest [17:58:34]: test autodep8-perl: /usr/share/pkg-perl-autopkgtest/runner runtime-deps
253s autopkgtest [17:58:34]: test autodep8-perl: [-----------------------
253s /usr/share/pkg-perl-autopkgtest/runtime-deps.d/use.t .. 
253s 1..4
253s ok 1 -  /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 exited successfully
253s ok 2 -  /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 produced no (non-whitelisted) output
253s ok 3 - env PERL_DL_NONLAZY=1  /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 exited successfully
253s ok 4 - env PERL_DL_NONLAZY=1  /usr/bin/perl -w -M"Bio::DB::HTS" -e 1 2>&1 produced no (non-whitelisted) output
253s ok
253s All tests successful.
253s Files=1, Tests=4,  0 wallclock secs ( 0.02 usr  0.01 sys +  0.23 cusr  0.07 csys =  0.33 CPU)
253s Result: PASS
254s autopkgtest [17:58:35]: test autodep8-perl: -----------------------]
254s autopkgtest [17:58:35]: test autodep8-perl:  - - - - - - - - - - results - - - - - - - - - -
254s autodep8-perl        PASS (superficial)
254s autopkgtest [17:58:35]: test autodep8-perl-recommends: preparing testbed
256s Reading package lists...
256s Building dependency tree...
256s Reading state information...
256s Starting pkgProblemResolver with broken count: 0
257s Starting 2 pkgProblemResolver with broken count: 0
257s Done
257s The following NEW packages will be installed:
257s   autopkgtest-satdep
257s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
257s Need to get 0 B/724 B of archives.
257s After this operation, 0 B of additional disk space will be used.
257s Get:1 /tmp/autopkgtest.qedwvw/3-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B]
258s Selecting previously unselected package autopkgtest-satdep.
258s (Reading database ... 
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258s Preparing to unpack .../3-autopkgtest-satdep.deb ...
258s Unpacking autopkgtest-satdep (0) ...
258s Setting up autopkgtest-satdep (0) ...
261s (Reading database ... 81058 files and directories currently installed.)
261s Removing autopkgtest-satdep (0) ...
262s autopkgtest [17:58:43]: test autodep8-perl-recommends: /usr/share/pkg-perl-autopkgtest/runner runtime-deps-and-recommends
262s autopkgtest [17:58:43]: test autodep8-perl-recommends: [-----------------------
263s /usr/share/pkg-perl-autopkgtest/runtime-deps-and-recommends.d/syntax.t .. 
263s 1..4
263s ok 1 - Package libbio-db-hts-perl is known to dpkg
263s ok 2 - Got status information for package libbio-db-hts-perl
263s ok 3 - Got file list for package libbio-db-hts-perl
263s # Subtest: all modules in libbio-db-hts-perl pass the syntax check
263s     1..22
263s     ok 1 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/AlignWrapper.pm exited successfully
263s     # Subroutine each_tag_value redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 461.
263s     # Subroutine get_tag_values redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 463.
263s     # Subroutine has_tag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 479.
263s     # Subroutine get_all_tags redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 495.
263s     # Subroutine start redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 502.
263s     # Subroutine end redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 508.
263s     # Subroutine stop redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 514.
263s     # Subroutine strand redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 517.
263s     # Subroutine abs_strand redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 521.
263s     # Subroutine mstrand redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 523.
263s     # Subroutine display_name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 528.
263s     # Subroutine qscore redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 532.
263s     # Subroutine qstring redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 539.
263s     # Subroutine primary_id redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 543.
263s     # Subroutine cigar_str redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 550.
263s     # Subroutine cigar_array redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 563.
263s     # Subroutine flag_str redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 577.
263s     # Subroutine length redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 586.
263s     # Subroutine mate_start redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 593.
263s     # Subroutine mate_len redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 599.
263s     # Subroutine mate_end redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 618.
263s     # Subroutine query redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 624.
263s     # Subroutine get_SeqFeatures redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 629.
263s     # Subroutine target redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 633.
263s     # Subroutine primary_tag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 638.
263s     # Subroutine source_tag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 639.
263s     # Subroutine hit redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm line 641.
263s     ok 2 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm exited successfully
263s     ok 3 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Constants.pm exited successfully
263s     ok 4 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Faidx.pm exited successfully
263s     ok 5 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/FetchIterator.pm exited successfully
263s     ok 6 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Record.pm exited successfully
263s     ok 7 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq.pm exited successfully
263s     ok 8 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Pileup.pm exited successfully
263s     ok 9 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/PileupWrapper.pm exited successfully
263s     # Constant subroutine Bio::DB::HTS::Query::CIGAR_SKIP redefined at /usr/lib/aarch64-linux-gnu/perl-base/constant.pm line 171.
263s     # Subroutine new redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 64.
263s     # Subroutine seq_id redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 76.
263s     # Subroutine name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 87.
263s     # Subroutine display_name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 98.
263s     # Subroutine primary_tag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 106.
263s     # Subroutine source_tag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 114.
263s     # Subroutine start redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 122.
263s     # Subroutine end redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 133.
263s     # Subroutine low redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 138.
263s     # Subroutine high redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 150.
263s     # Subroutine length redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 171.
263s     # Subroutine seq redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 184.
263s     # Subroutine qscore redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 198.
263s     # Subroutine dna redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 210.
263s     # Subroutine strand redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 221.
263s     # Subroutine subseq redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm line 233.
263s     ok 10 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm exited successfully
263s     ok 11 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/ReadIterator.pm exited successfully
263s     # Name "Bio::DB::HTS::Segment::sourceseq" used only once: possible typo at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm line 70.
263s     # Name "Bio::DB::HTS::Segment::abs_ref" used only once: possible typo at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm line 70.
263s     # Name "Bio::DB::HTS::Segment::ref" used only once: possible typo at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm line 70.
263s     ok 12 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm exited successfully
263s     ok 13 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix/Iterator.pm exited successfully
263s     ok 14 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix.pm exited successfully
263s     # Subroutine dna redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 43.
263s     # Subroutine qscore redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 49.
263s     # Subroutine start redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 56.
263s     # Subroutine end redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 61.
263s     # Subroutine reversec redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm line 68.
263s     ok 15 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm exited successfully
263s     ok 16 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Header.pm exited successfully
263s     ok 17 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/HeaderPtr.pm exited successfully
263s     ok 18 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Iterator.pm exited successfully
263s     ok 19 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Row.pm exited successfully
263s     ok 20 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/RowPtr.pm exited successfully
263s     ok 21 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF.pm exited successfully
263s     # Constant subroutine Bio::DB::HTS::DUMP_INTERVAL redefined at /usr/lib/aarch64-linux-gnu/perl-base/constant.pm line 171.
263s     # Subroutine new redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1375.
263s     # Subroutine hts_file redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1409.
263s     # Subroutine clone redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1412.
263s     # Subroutine header redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1420.
263s     # Subroutine hts_path redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1426.
263s     # Subroutine fai redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1431.
263s     # Subroutine new_dna_accessor redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1433.
263s     # Subroutine can_do_seq redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1455.
263s     # Subroutine seq redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1462.
263s     # Subroutine expand_flags redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1473.
263s     # Subroutine split_splices redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1480.
263s     # Subroutine autoindex redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1487.
263s     # Subroutine force_refseq redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1494.
263s     # Subroutine n_targets redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1501.
263s     # Subroutine target_name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1505.
263s     # Subroutine target_len redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1512.
263s     # Subroutine seq_ids redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1519.
263s     # Subroutine _cache_targets redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1524.
263s     # Subroutine length redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1535.
263s     # Subroutine _fetch redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1541.
263s     # Subroutine fetch redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1554.
263s     # Subroutine pileup redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1566.
263s     # Subroutine fast_pileup redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1588.
263s     # Subroutine segment redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1611.
263s     # Subroutine get_features_by_location redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1636.
263s     # Subroutine get_features_by_attribute redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1652.
263s     # Subroutine get_features_by_tag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1658.
263s     # Subroutine get_features_by_flag redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1662.
263s     # Subroutine get_feature_by_name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1666.
263s     # Subroutine get_features_by_name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1678.
263s     # Subroutine get_feature_by_id redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1680.
263s     # Subroutine get_seq_stream redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1698.
263s     # Subroutine get_seq_fh redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1703.
263s     # Subroutine types redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1708.
263s     # Subroutine features redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1712.
263s     # Subroutine coverage2BedGraph redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1816.
263s     # Subroutine _filter_features redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1860.
263s     # Subroutine _push_features redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1904.
263s     # Subroutine last_feature_count redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1928.
263s     # Subroutine _features redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1930.
263s     # Subroutine _build_mates redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 1950.
263s     # Subroutine _coverage redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2000.
263s     # Subroutine _segment_search redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2038.
263s     # Subroutine hts_index redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2053.
263s     # Subroutine _features_fh redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2062.
263s     # Subroutine tam_fh redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2076.
263s     # Subroutine max_pileup_cnt redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2081.
263s     # Subroutine _filter_by_name redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2088.
263s     # Subroutine _filter_by_attribute redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2104.
263s     # Subroutine _glob_match redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2132.
263s     # Subroutine open redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2146.
263s     # Subroutine seq redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2148.
263s     # Subroutine coverage redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2163.
263s     # Subroutine source redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2169.
263s     # Subroutine method redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2176.
263s     # Subroutine gff3_string redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2183.
263s     # Subroutine index redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2199.
263s     # Ambiguous call resolved as CORE::open(), qualify as such or use & at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2238.
263s     # Ambiguous call resolved as CORE::open(), qualify as such or use & at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2243.
263s     # Subroutine reindex redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2230.
263s     # Subroutine index_open_in_safewd redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2269.
263s     # Subroutine mtime redefined at /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm line 2280.
263s     ok 22 - /usr/bin/perl -wc /usr/lib/aarch64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm exited successfully
263s ok 4 - all modules in libbio-db-hts-perl pass the syntax check
263s ok
263s All tests successful.
263s Files=1, Tests=4,  1 wallclock secs ( 0.03 usr  0.00 sys +  1.07 cusr  0.26 csys =  1.36 CPU)
263s Result: PASS
264s autopkgtest [17:58:45]: test autodep8-perl-recommends: -----------------------]
264s autodep8-perl-recommends PASS (superficial)
264s autopkgtest [17:58:45]: test autodep8-perl-recommends:  - - - - - - - - - - results - - - - - - - - - -
265s autopkgtest [17:58:46]: @@@@@@@@@@@@@@@@@@@@ summary
265s autodep8-perl-build-deps PASS
265s autodep8-perl        PASS (superficial)
265s autodep8-perl-recommends PASS (superficial)
277s nova [W] Skipping flock in bos03-arm64
277s Creating nova instance adt-plucky-arm64-libbio-db-hts-perl-20241101-175420-juju-7f2275-prod-proposed-migration-environment-15-5e7a0627-f71a-4b93-a669-7b507d6a3e48 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...
277s nova [W] Skipping flock in bos03-arm64
277s Creating nova instance adt-plucky-arm64-libbio-db-hts-perl-20241101-175420-juju-7f2275-prod-proposed-migration-environment-15-5e7a0627-f71a-4b93-a669-7b507d6a3e48 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...