0s autopkgtest [14:07:50]: starting date and time: 2024-03-20 14:07:50+0000
  0s autopkgtest [14:07:50]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [14:07:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s0rhi_27/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:crac,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade crac --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=crac/2.5.2+dfsg-6 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-13.secgroup --name adt-noble-ppc64el-crac-20240320-140750-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
116s autopkgtest [14:09:46]: testbed dpkg architecture: ppc64el
116s autopkgtest [14:09:46]: testbed apt version: 2.7.12
116s autopkgtest [14:09:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup
117s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
117s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
118s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
118s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB]
118s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3804 kB]
118s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [669 kB]
118s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
118s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
118s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
118s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4153 kB]
118s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
118s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.7 kB]
118s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
121s Fetched 9360 kB in 2s (4282 kB/s)
122s Reading package lists...
124s Reading package lists...
124s Building dependency tree...
124s Reading state information...
124s Calculating upgrade...
125s The following packages will be REMOVED:
125s   libssl3
125s The following NEW packages will be installed:
125s   libssl3t64
125s The following packages have been kept back:
125s   curl
125s The following packages will be upgraded:
125s   openssl
125s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
125s Need to get 3151 kB of archives.
125s After this operation, 73.7 kB of additional disk space will be used.
125s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu2 [1026 kB]
125s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu2 [2125 kB]
125s Fetched 3151 kB in 1s (4463 kB/s)
126s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70095 files and directories currently installed.)
126s Preparing to unpack .../openssl_3.0.13-0ubuntu2_ppc64el.deb ...
126s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ...
126s dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested:
126s  wget depends on libssl3 (>= 3.0.0).
126s  tnftp depends on libssl3 (>= 3.0.0).
126s  tcpdump depends on libssl3 (>= 3.0.0).
126s  systemd-resolved depends on libssl3 (>= 3.0.0).
126s  systemd depends on libssl3 (>= 3.0.0).
126s  sudo depends on libssl3 (>= 3.0.0).
126s  rsync depends on libssl3 (>= 3.0.0).
126s  python3-cryptography depends on libssl3 (>= 3.0.0).
126s  openssh-server depends on libssl3 (>= 3.0.10).
126s  openssh-client depends on libssl3 (>= 3.0.10).
126s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
126s  libsystemd-shared:ppc64el depends on libssl3 (>= 3.0.0).
126s  libssh-4:ppc64el depends on libssl3 (>= 3.0.0).
126s  libsasl2-modules:ppc64el depends on libssl3 (>= 3.0.0).
126s  libsasl2-2:ppc64el depends on libssl3 (>= 3.0.0).
126s  libpython3.12-minimal:ppc64el depends on libssl3 (>= 3.0.0).
126s  libpython3.11-minimal:ppc64el depends on libssl3 (>= 3.0.0).
126s  libnvme1 depends on libssl3 (>= 3.0.0).
126s  libkrb5-3:ppc64el depends on libssl3 (>= 3.0.0).
126s  libkmod2:ppc64el depends on libssl3 (>= 3.0.0).
126s  libfido2-1:ppc64el depends on libssl3 (>= 3.0.0).
126s  libcurl4:ppc64el depends on libssl3 (>= 3.0.0).
126s  libcryptsetup12:ppc64el depends on libssl3 (>= 3.0.0).
126s  kmod depends on libssl3 (>= 3.0.0).
126s  dhcpcd-base depends on libssl3 (>= 3.0.0).
126s  bind9-libs:ppc64el depends on libssl3 (>= 3.0.0).
126s 
126s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70095 files and directories currently installed.)
126s Removing libssl3:ppc64el (3.0.10-1ubuntu4) ...
126s Selecting previously unselected package libssl3t64:ppc64el.
126s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70084 files and directories currently installed.)
126s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_ppc64el.deb ...
126s Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
126s Setting up libssl3t64:ppc64el (3.0.13-0ubuntu2) ...
126s Setting up openssl (3.0.13-0ubuntu2) ...
126s Processing triggers for man-db (2.12.0-3) ...
127s Processing triggers for libc-bin (2.39-0ubuntu2) ...
127s Reading package lists...
127s Building dependency tree...
127s Reading state information...
127s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
127s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
127s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
128s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
128s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
129s Reading package lists...
129s Reading package lists...
129s Building dependency tree...
129s Reading state information...
129s Calculating upgrade...
129s The following packages have been kept back:
129s   curl
129s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
129s Reading package lists...
130s Building dependency tree...
130s Reading state information...
130s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
133s autopkgtest [14:10:03]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
133s autopkgtest [14:10:03]: @@@@@@@@@@@@@@@@@@@@ apt-source crac
135s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe crac 2.5.2+dfsg-6 (dsc) [2080 B]
135s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe crac 2.5.2+dfsg-6 (tar) [658 kB]
135s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe crac 2.5.2+dfsg-6 (diff) [15.2 kB]
135s gpgv: Signature made Tue Mar 19 17:30:31 2024 UTC
135s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
135s gpgv: Can't check signature: No public key
135s dpkg-source: warning: cannot verify inline signature for ./crac_2.5.2+dfsg-6.dsc: no acceptable signature found
135s autopkgtest [14:10:05]: testing package crac version 2.5.2+dfsg-6
135s autopkgtest [14:10:05]: build not needed
136s autopkgtest [14:10:06]: test run-unit-test: preparing testbed
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s Starting pkgProblemResolver with broken count: 0
139s Starting 2 pkgProblemResolver with broken count: 0
139s Done
140s The following additional packages will be installed:
140s   crac curl libcurl3t64-gnutls libcurl4t64 libdeflate0 libgkarrays1t64
140s   libgnutls30t64 libgzstream0 libhogweed6t64 libhts3t64 libhtscodecs2
140s   libjellyfish-2.0-2 libnettle8t64 libpsl5t64
140s Suggested packages:
140s   gnutls-bin
140s The following packages will be REMOVED:
140s   libcurl3-gnutls libcurl4 libgnutls30 libhogweed6 libnettle8 libpsl5
140s The following NEW packages will be installed:
140s   autopkgtest-satdep crac libcurl3t64-gnutls libcurl4t64 libdeflate0
140s   libgkarrays1t64 libgnutls30t64 libgzstream0 libhogweed6t64 libhts3t64
140s   libhtscodecs2 libjellyfish-2.0-2 libnettle8t64 libpsl5t64
140s The following packages will be upgraded:
140s   curl
140s 1 upgraded, 14 newly installed, 6 to remove and 0 not upgraded.
140s Need to get 4188 kB/4189 kB of archives.
140s After this operation, 5905 kB of additional disk space will be used.
140s Get:1 /tmp/autopkgtest.x3CRH6/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B]
140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2 [226 kB]
140s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2 [208 kB]
140s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu2 [1154 kB]
141s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl4t64 ppc64el 8.5.0-2ubuntu7 [428 kB]
141s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el curl ppc64el 8.5.0-2ubuntu7 [234 kB]
141s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpsl5t64 ppc64el 0.21.2-1.1 [59.0 kB]
141s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl3t64-gnutls ppc64el 8.5.0-2ubuntu7 [419 kB]
141s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgkarrays1t64 ppc64el 2.1.0+dfsg-4.2 [60.8 kB]
141s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libgzstream0 ppc64el 1.5+git20171107.9a20658-1 [7734 B]
141s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
141s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB]
141s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libhts3t64 ppc64el 1.19+ds-1.1build2 [569 kB]
141s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el libjellyfish-2.0-2 ppc64el 2.3.1-2build1 [75.7 kB]
141s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el crac ppc64el 2.5.2+dfsg-6 [576 kB]
141s Fetched 4188 kB in 1s (3297 kB/s)
141s dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested:
141s  librtmp1:ppc64el depends on libhogweed6.
141s  libjcat1:ppc64el depends on libhogweed6.
141s  libgnutls30:ppc64el depends on libhogweed6 (>= 3.6).
141s 
141s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70097 files and directories currently installed.)
141s Removing libhogweed6:ppc64el (3.9.1-2) ...
141s dpkg: libnettle8:ppc64el: dependency problems, but removing anyway as you requested:
141s  librtmp1:ppc64el depends on libnettle8.
141s  libgnutls30:ppc64el depends on libnettle8 (>= 3.9~).
141s  libcurl3-gnutls:ppc64el depends on libnettle8.
141s  libarchive13:ppc64el depends on libnettle8.
141s 
141s Removing libnettle8:ppc64el (3.9.1-2) ...
141s Selecting previously unselected package libnettle8t64:ppc64el.
141s (Reading database ... 
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(Reading database ... 70085 files and directories currently installed.)
141s Preparing to unpack .../libnettle8t64_3.9.1-2.2_ppc64el.deb ...
141s Unpacking libnettle8t64:ppc64el (3.9.1-2.2) ...
141s Selecting previously unselected package libhogweed6t64:ppc64el.
141s Preparing to unpack .../libhogweed6t64_3.9.1-2.2_ppc64el.deb ...
141s Unpacking libhogweed6t64:ppc64el (3.9.1-2.2) ...
141s dpkg: libgnutls30:ppc64el: dependency problems, but removing anyway as you requested:
141s  librtmp1:ppc64el depends on libgnutls30 (>= 3.7.2).
141s  libldap2:ppc64el depends on libgnutls30 (>= 3.8.2).
141s  libjcat1:ppc64el depends on libgnutls30 (>= 3.7.3).
141s  libcurl3-gnutls:ppc64el depends on libgnutls30 (>= 3.8.2).
141s  fwupd depends on libgnutls30 (>= 3.7.3).
141s  dirmngr depends on libgnutls30 (>= 3.8.1).
141s  apt depends on libgnutls30 (>= 3.8.1).
141s 
141s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70099 files and directories currently installed.)
141s Removing libgnutls30:ppc64el (3.8.3-1ubuntu1) ...
141s Selecting previously unselected package libgnutls30t64:ppc64el.
141s (Reading database ... 
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(Reading database ... 70090 files and directories currently installed.)
141s Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_ppc64el.deb ...
141s Unpacking libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ...
142s dpkg: libcurl4:ppc64el: dependency problems, but removing anyway as you requested:
142s  curl depends on libcurl4 (= 8.5.0-2ubuntu2).
142s 
142s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70118 files and directories currently installed.)
142s Removing libcurl4:ppc64el (8.5.0-2ubuntu2) ...
142s Selecting previously unselected package libcurl4t64:ppc64el.
142s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70113 files and directories currently installed.)
142s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu7_ppc64el.deb ...
142s Unpacking libcurl4t64:ppc64el (8.5.0-2ubuntu7) ...
142s Preparing to unpack .../curl_8.5.0-2ubuntu7_ppc64el.deb ...
142s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ...
142s dpkg: libpsl5:ppc64el: dependency problems, but removing anyway as you requested:
142s  wget depends on libpsl5 (>= 0.16.0).
142s  libcurl3-gnutls:ppc64el depends on libpsl5 (>= 0.16.0).
142s 
142s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70119 files and directories currently installed.)
142s Removing libpsl5:ppc64el (0.21.2-1build1) ...
142s Selecting previously unselected package libpsl5t64:ppc64el.
142s (Reading database ... 
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(Reading database ... 50%
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(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 ... 70114 files and directories currently installed.)
142s Preparing to unpack .../libpsl5t64_0.21.2-1.1_ppc64el.deb ...
142s Unpacking libpsl5t64:ppc64el (0.21.2-1.1) ...
142s dpkg: libcurl3-gnutls:ppc64el: dependency problems, but removing anyway as you requested:
142s  libfwupd2:ppc64el depends on libcurl3-gnutls (>= 7.63.0).
142s  fwupd depends on libcurl3-gnutls (>= 7.63.0).
142s 
142s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70120 files and directories currently installed.)
142s Removing libcurl3-gnutls:ppc64el (8.5.0-2ubuntu2) ...
142s Selecting previously unselected package libcurl3t64-gnutls:ppc64el.
142s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70113 files and directories currently installed.)
142s Preparing to unpack .../0-libcurl3t64-gnutls_8.5.0-2ubuntu7_ppc64el.deb ...
142s Unpacking libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu7) ...
142s Selecting previously unselected package libgkarrays1t64.
142s Preparing to unpack .../1-libgkarrays1t64_2.1.0+dfsg-4.2_ppc64el.deb ...
142s Unpacking libgkarrays1t64 (2.1.0+dfsg-4.2) ...
142s Selecting previously unselected package libgzstream0:ppc64el.
142s Preparing to unpack .../2-libgzstream0_1.5+git20171107.9a20658-1_ppc64el.deb ...
142s Unpacking libgzstream0:ppc64el (1.5+git20171107.9a20658-1) ...
142s Selecting previously unselected package libdeflate0:ppc64el.
142s Preparing to unpack .../3-libdeflate0_1.19-1_ppc64el.deb ...
142s Unpacking libdeflate0:ppc64el (1.19-1) ...
142s Selecting previously unselected package libhtscodecs2:ppc64el.
142s Preparing to unpack .../4-libhtscodecs2_1.6.0-1_ppc64el.deb ...
142s Unpacking libhtscodecs2:ppc64el (1.6.0-1) ...
142s Selecting previously unselected package libhts3t64:ppc64el.
142s Preparing to unpack .../5-libhts3t64_1.19+ds-1.1build2_ppc64el.deb ...
142s Unpacking libhts3t64:ppc64el (1.19+ds-1.1build2) ...
142s Selecting previously unselected package libjellyfish-2.0-2:ppc64el.
142s Preparing to unpack .../6-libjellyfish-2.0-2_2.3.1-2build1_ppc64el.deb ...
142s Unpacking libjellyfish-2.0-2:ppc64el (2.3.1-2build1) ...
142s Selecting previously unselected package crac.
142s Preparing to unpack .../7-crac_2.5.2+dfsg-6_ppc64el.deb ...
142s Unpacking crac (2.5.2+dfsg-6) ...
142s Selecting previously unselected package autopkgtest-satdep.
142s Preparing to unpack .../8-1-autopkgtest-satdep.deb ...
142s Unpacking autopkgtest-satdep (0) ...
142s Setting up libhtscodecs2:ppc64el (1.6.0-1) ...
142s Setting up libpsl5t64:ppc64el (0.21.2-1.1) ...
142s Setting up libdeflate0:ppc64el (1.19-1) ...
142s Setting up libgkarrays1t64 (2.1.0+dfsg-4.2) ...
142s Setting up libjellyfish-2.0-2:ppc64el (2.3.1-2build1) ...
142s Setting up libnettle8t64:ppc64el (3.9.1-2.2) ...
142s Setting up libgzstream0:ppc64el (1.5+git20171107.9a20658-1) ...
142s Setting up libhogweed6t64:ppc64el (3.9.1-2.2) ...
142s Setting up libgnutls30t64:ppc64el (3.8.3-1.1ubuntu2) ...
142s Setting up libcurl4t64:ppc64el (8.5.0-2ubuntu7) ...
142s Setting up libcurl3t64-gnutls:ppc64el (8.5.0-2ubuntu7) ...
142s Setting up libhts3t64:ppc64el (1.19+ds-1.1build2) ...
142s Setting up crac (2.5.2+dfsg-6) ...
142s Setting up curl (8.5.0-2ubuntu7) ...
142s Setting up autopkgtest-satdep (0) ...
142s Processing triggers for man-db (2.12.0-3) ...
142s Processing triggers for libc-bin (2.39-0ubuntu2) ...
145s (Reading database ... 70292 files and directories currently installed.)
145s Removing autopkgtest-satdep (0) ...
145s autopkgtest [14:10:15]: test run-unit-test: [-----------------------
147s Launching ' crac -i ../../test_f/causes/genome -r snp.fa -k 22 --deep-snv --nb-nucleotides-snv-comparison 3 -o ../../test_f/causes/snp.sam --detailed-sam --use-x-in-cigar'
147s ==> ../../test_f/causes/snp.fa.tap
147s 
147s Launching ' crac -i ../../test_f/causes/genome -r biotag.fa -k 22 -o ../../test_f/causes/biotag.sam --detailed-sam --use-x-in-cigar'
147s ==> ../../test_f/causes/biotag.fa.tap
147s 
147s Launching ' crac -i ../../test_f/splices_adjust/genome -r splice.fa -k 22 -o ../../test_f/splices_adjust/splice.sam --detailed-sam'
147s ==> ../../test_f/splices_adjust/splice.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-16403-genome -r bug-16403-read.fa -k 20 -o ../../test_f/bug/bug-16931.sam'
147s ==> ../../test_f/bug/bug-16931.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15605-genome -r bug-15605-read.fa -k 22 -o ../../test_f/bug/bug-15605.sam --detailed-sam'
147s ==> ../../test_f/bug/bug-15605.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18409-genome -r bug-18409-read.fa --detailed-sam -k 22 -o /dev/stdout | tr ';' '\n''
147s ==> ./bug-18409.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18435-genome -r bug-18435-read.fa -k 22 -o ../../test_f/bug/bug-18435.sam'
147s ==> ../../test_f/bug/bug-18435.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18522-genome -r bug-18522-read.fa -k 10 -o ../../test_f/bug/bug-18522.sam --treat-multiple 2'
147s ==> ../../test_f/bug/bug-18522.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-17749-genome -r bug-17749-read.fa -k 22 -o ../../test_f/bug/bug-17749.sam --max-splice-length 100 --max-extension-length 2 --min-chimera-score 0'
147s ==> ../../test_f/bug/bug-17749.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-2015-12-08-genome -r bug-2015-12-08-read1.fa bug-2015-12-08-read2.fa -k 22 -o ../../test_f/bug/bug-2015-12-08.sam --detailed-sam --reads-index GKARRAYS'
147s ==> ../../test_f/bug/bug-2015-12-08.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15677-genome -r bug-15677-read.fa -k 22 -o ../../test_f/bug/bug-15677.sam'
147s ==> ../../test_f/bug/bug-15677.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15630-genome -r bug-15630-read.fa --detailed-sam -k 18 -o ../../test_f/bug/bug-15630.sam'
147s ==> ../../test_f/bug/bug-15630.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15649-genome-2 -r bug-15649-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15649-2.sam'
147s ==> ../../test_f/bug/bug-15649-2.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-16581-genome -r bug-16581-read.fq -m 25 -k 22 -o ../../test_f/bug/bug-16581.sam'
147s ==> ../../test_f/bug/bug-16581.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15847-genome -r bug-15847-read.fa -k 22 --treat-multiple 36 --detailed-sam -o ../../test_f/bug/bug-15847.sam'
147s ==> ../../test_f/bug/bug-15847.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18793-genome -r bug-18793-read.fa -k 22 -o ../../test_f/bug/bug-18793.sam --detailed-sam --reads-index GKARRAYS'
147s ==> ../../test_f/bug/bug-18793.tap
147s 
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15672-genome -r bug-15672-read.fa -k 22 -o ../../test_f/bug/bug-15672.sam --detailed-sam'
147s ==> ../../test_f/bug/bug-15672.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-17175-genome -r bug-17175-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-17175.sam --use-x-in-cigar'
147s ==> ../../test_f/bug/bug-17175.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18180-genome -r bug-18180-read.fa --detailed-sam --emt -k 18 -o ../../test_f/bug/bug-18180.sam'
147s Warning: Running CRAC--emt with k=18 which means that it only maps the first located kmer of length 18 for each read
147s ==> ../../test_f/bug/bug-18180.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15639-genome -r bug-15639-read.fa -k 22 -o ../../test_f/bug/bug-15639.sam'
147s ==> ../../test_f/bug/bug-15639.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-16502-genome -r bug-16502-read.fa -k 22 -o ../../test_f/bug/bug-16502.sam --reads-index GKARRAYS'
147s ==> ../../test_f/bug/bug-16502.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-case-sensitive-genome -r bug-case-sensitive-read.fa -k 12 -o ../../test_f/bug/bug-case-sensitive.sam --detailed-sam'
147s ==> ../../test_f/bug/bug-case-sensitive.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18524-genome -r bug-18524-read.fa -k 22 -o ../../test_f/bug/bug-18524.sam --detailed-sam'
147s ==> ../../test_f/bug/bug-18524.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15649-genome -r bug-15649-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15649.sam'
147s ==> ../../test_f/bug/bug-15649.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-18568-genome -r bug-18568-read.fa -k 22 -o ../../test_f/bug/bug-18568.sam --detailed-sam --reads-index GKARRAYS'
147s ==> ../../test_f/bug/bug-18568.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15646-genome -r bug-15646-read.fa --detailed-sam -k 22 -o ../../test_f/bug/bug-15646.sam'
147s ==> ../../test_f/bug/bug-15646.tap
147s 
147s Launching ' crac -i ../../test_f/bug/bug-15605_2-genome -r bug-15605_2-read.fa -k 22 -o ../../test_f/bug/bug-15605_2.sam --detailed-sam'
147s ==> ../../test_f/bug/bug-15605_2.tap
147s 
147s Launching ' crac -i ../../test_f/cigar/genome -r reads_sam1.fasta reads_sam2.fasta -k 10 -o ../../test_f/cigar/consistency3.sam --treat-multiple 100 --use-x-in-cigar'
147s ==> ../../test_f/cigar/consistency3.tap
147s 
147s Launching ' crac -i ../../test_f/cigar/genome -r reads_k18.fasta -k 18 -o ../../test_f/cigar/consistency2.sam'
147s ==> ../../test_f/cigar/consistency2.tap
147s 
147s Launching ' crac -i ../../test_f/cigar/genome -r reads.fasta -k 22 -o ../../test_f/cigar/consistency.sam --detailed-sam --reads-index GKARRAYS --use-x-in-cigar --min-chimera-score 0'
147s ==> ../../test_f/cigar/consistency.tap
148s 
148s autopkgtest [14:10:18]: test run-unit-test: -----------------------]
149s run-unit-test        PASS
149s autopkgtest [14:10:19]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
149s autopkgtest [14:10:19]: @@@@@@@@@@@@@@@@@@@@ summary
149s run-unit-test        PASS
161s Creating nova instance adt-noble-ppc64el-crac-20240320-140750-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240320.img (UUID 1c7ceb83-4842-4144-a3c9-88510cdc9534)...