0s autopkgtest [17:14:40]: starting date and time: 2024-03-16 17:14:40+0000
  0s autopkgtest [17:14:40]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [17:14:40]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ds5b9tiw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib,src:curl,src:gnutls28,src:libpsl,src:nettle,src:openssl --apt-upgrade rsem --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=htslib/1.19+ds-1.1build2 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-arm64-17.secgroup --name adt-noble-arm64-rsem-20240316-171440-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
108s autopkgtest [17:16:28]: testbed dpkg architecture: arm64
108s autopkgtest [17:16:28]: testbed apt version: 2.7.12
108s autopkgtest [17:16:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup
110s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
110s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB]
111s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
111s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB]
111s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
111s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
111s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
111s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
111s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
111s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB]
111s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
111s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB]
111s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
117s Fetched 9063 kB in 3s (2961 kB/s)
117s Reading package lists...
122s Reading package lists...
122s Building dependency tree...
122s 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 2753 kB of archives.
125s After this operation, 72.7 kB of additional disk space will be used.
125s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
125s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
127s Fetched 2753 kB in 1s (2478 kB/s)
127s (Reading database ... 
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(Reading database ... 95%
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(Reading database ... 75850 files and directories currently installed.)
127s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
127s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
127s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
127s  wget depends on libssl3 (>= 3.0.0).
127s  u-boot-tools depends on libssl3 (>= 3.0.0).
127s  tnftp depends on libssl3 (>= 3.0.0).
127s  tcpdump depends on libssl3 (>= 3.0.0).
127s  systemd-resolved depends on libssl3 (>= 3.0.0).
127s  systemd depends on libssl3 (>= 3.0.0).
127s  sudo depends on libssl3 (>= 3.0.0).
127s  sbsigntool depends on libssl3 (>= 3.0.0).
127s  rsync depends on libssl3 (>= 3.0.0).
127s  python3-cryptography depends on libssl3 (>= 3.0.0).
127s  openssh-server depends on libssl3 (>= 3.0.10).
127s  openssh-client depends on libssl3 (>= 3.0.10).
127s  mtd-utils depends on libssl3 (>= 3.0.0).
127s  mokutil depends on libssl3 (>= 3.0.0).
127s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
127s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
127s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
127s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
127s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
127s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
127s  libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0).
127s  libnvme1 depends on libssl3 (>= 3.0.0).
127s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
127s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
127s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
127s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
127s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
127s  kmod depends on libssl3 (>= 3.0.0).
127s  dhcpcd-base depends on libssl3 (>= 3.0.0).
127s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
127s 
127s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75850 files and directories currently installed.)
127s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
127s Selecting previously unselected package libssl3t64:arm64.
127s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75839 files and directories currently installed.)
127s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
127s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
128s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
128s Setting up openssl (3.0.13-0ubuntu1) ...
128s Processing triggers for man-db (2.12.0-3) ...
129s Processing triggers for libc-bin (2.39-0ubuntu2) ...
129s Reading package lists...
130s Building dependency tree...
130s Reading state information...
131s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
131s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
132s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
132s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
132s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
135s Reading package lists...
135s Reading package lists...
136s Building dependency tree...
136s Reading state information...
138s Calculating upgrade...
138s The following packages have been kept back:
138s   curl
138s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
138s Reading package lists...
139s Building dependency tree...
139s Reading state information...
140s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
144s autopkgtest [17:17:04]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
144s autopkgtest [17:17:04]: @@@@@@@@@@@@@@@@@@@@ apt-source rsem
149s Get:1 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (dsc) [2249 B]
149s Get:2 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (tar) [275 kB]
149s Get:3 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (diff) [35.7 MB]
150s gpgv: Signature made Mon Dec 18 13:04:45 2023 UTC
150s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
150s gpgv:                issuer "emollier@debian.org"
150s gpgv: Can't check signature: No public key
150s dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found
151s autopkgtest [17:17:11]: testing package rsem version 1.3.3+dfsg-3
154s autopkgtest [17:17:14]: build not needed
155s autopkgtest [17:17:15]: test run-unit-test: preparing testbed
160s Reading package lists...
161s Building dependency tree...
161s Reading state information...
162s Starting pkgProblemResolver with broken count: 0
162s Starting 2 pkgProblemResolver with broken count: 0
162s Done
163s The following additional packages will be installed:
163s   bowtie fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
163s   libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5
163s   libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0
163s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
163s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
163s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
163s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
163s   r-base-core rsem unzip x11-common xdg-utils zip
163s Suggested packages:
163s   bowtie-examples tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib
163s   r-base-html r-bioc-ebseq hisat2
163s Recommended packages:
163s   r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl
163s   libx11-protocol-perl x11-utils x11-xserver-utils
163s The following NEW packages will be installed:
163s   autopkgtest-satdep bowtie fontconfig fontconfig-config fonts-dejavu-core
163s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
163s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2
163s   libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
163s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
163s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
163s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
163s   r-base-core rsem unzip x11-common xdg-utils zip
163s 0 upgraded, 49 newly installed, 0 to remove and 1 not upgraded.
163s Need to get 74.5 MB/74.5 MB of archives.
163s After this operation, 120 MB of additional disk space will be used.
163s Get:1 /tmp/autopkgtest.ilYrHy/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B]
163s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
164s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
164s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
164s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
164s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
164s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
164s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
164s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
164s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
164s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
164s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
164s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
164s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
164s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
164s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
164s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
164s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
164s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
164s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhts3 arm64 1.19+ds-1 [429 kB]
164s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
164s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB]
164s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
164s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
164s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
164s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
164s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
164s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
164s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
164s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
164s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
164s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB]
164s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B]
164s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
164s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB]
164s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
165s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
165s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
165s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
165s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
165s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
165s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
165s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB]
165s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB]
165s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB]
165s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
165s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB]
166s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie arm64 1.3.1-3 [1346 kB]
166s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 rsem arm64 1.3.3+dfsg-3 [36.0 MB]
167s Preconfiguring packages ...
168s Fetched 74.5 MB in 3s (22.1 MB/s)
168s Selecting previously unselected package fonts-dejavu-mono.
168s (Reading database ... 
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75852 files and directories currently installed.)
168s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ...
168s Unpacking fonts-dejavu-mono (2.37-8) ...
168s Selecting previously unselected package fonts-dejavu-core.
168s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ...
168s Unpacking fonts-dejavu-core (2.37-8) ...
168s Selecting previously unselected package fontconfig-config.
168s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
169s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
169s Selecting previously unselected package libfontconfig1:arm64.
169s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
169s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
169s Selecting previously unselected package fontconfig.
169s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
169s Unpacking fontconfig (2.15.0-1ubuntu1) ...
169s Selecting previously unselected package libblas3:arm64.
169s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ...
169s Unpacking libblas3:arm64 (3.12.0-3) ...
169s Selecting previously unselected package libpixman-1-0:arm64.
169s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_arm64.deb ...
169s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
169s Selecting previously unselected package libxcb-render0:arm64.
169s Preparing to unpack .../07-libxcb-render0_1.15-1_arm64.deb ...
169s Unpacking libxcb-render0:arm64 (1.15-1) ...
169s Selecting previously unselected package libxcb-shm0:arm64.
169s Preparing to unpack .../08-libxcb-shm0_1.15-1_arm64.deb ...
169s Unpacking libxcb-shm0:arm64 (1.15-1) ...
169s Selecting previously unselected package libxrender1:arm64.
169s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
169s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
169s Selecting previously unselected package libcairo2:arm64.
169s Preparing to unpack .../10-libcairo2_1.18.0-1_arm64.deb ...
169s Unpacking libcairo2:arm64 (1.18.0-1) ...
169s Selecting previously unselected package libdatrie1:arm64.
169s Preparing to unpack .../11-libdatrie1_0.2.13-3_arm64.deb ...
169s Unpacking libdatrie1:arm64 (0.2.13-3) ...
169s Selecting previously unselected package libdeflate0:arm64.
169s Preparing to unpack .../12-libdeflate0_1.19-1_arm64.deb ...
169s Unpacking libdeflate0:arm64 (1.19-1) ...
169s Selecting previously unselected package libgfortran5:arm64.
169s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
169s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
170s Selecting previously unselected package libgomp1:arm64.
170s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
170s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
170s Selecting previously unselected package libgraphite2-3:arm64.
170s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_arm64.deb ...
170s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
170s Selecting previously unselected package libharfbuzz0b:arm64.
170s Preparing to unpack .../16-libharfbuzz0b_8.3.0-2_arm64.deb ...
170s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
170s Selecting previously unselected package libhtscodecs2:arm64.
170s Preparing to unpack .../17-libhtscodecs2_1.6.0-1_arm64.deb ...
170s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
170s Selecting previously unselected package libhts3:arm64.
170s Preparing to unpack .../18-libhts3_1.19+ds-1_arm64.deb ...
170s Unpacking libhts3:arm64 (1.19+ds-1) ...
170s Selecting previously unselected package x11-common.
170s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu2_all.deb ...
170s Unpacking x11-common (1:7.7+23ubuntu2) ...
170s Selecting previously unselected package libice6:arm64.
170s Preparing to unpack .../20-libice6_2%3a1.0.10-1build2_arm64.deb ...
170s Unpacking libice6:arm64 (2:1.0.10-1build2) ...
170s Selecting previously unselected package libjpeg-turbo8:arm64.
170s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
170s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
170s Selecting previously unselected package libjpeg8:arm64.
170s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ...
170s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
170s Selecting previously unselected package liblapack3:arm64.
170s Preparing to unpack .../23-liblapack3_3.12.0-3_arm64.deb ...
170s Unpacking liblapack3:arm64 (3.12.0-3) ...
171s Selecting previously unselected package liblerc4:arm64.
171s Preparing to unpack .../24-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
171s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
171s Selecting previously unselected package libthai-data.
171s Preparing to unpack .../25-libthai-data_0.1.29-2_all.deb ...
171s Unpacking libthai-data (0.1.29-2) ...
171s Selecting previously unselected package libthai0:arm64.
171s Preparing to unpack .../26-libthai0_0.1.29-2_arm64.deb ...
171s Unpacking libthai0:arm64 (0.1.29-2) ...
171s Selecting previously unselected package libpango-1.0-0:arm64.
171s Preparing to unpack .../27-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
171s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
171s Selecting previously unselected package libpangoft2-1.0-0:arm64.
171s Preparing to unpack .../28-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ...
171s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
171s Selecting previously unselected package libpangocairo-1.0-0:arm64.
171s Preparing to unpack .../29-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ...
171s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
171s Selecting previously unselected package libpaper1:arm64.
171s Preparing to unpack .../30-libpaper1_1.1.29_arm64.deb ...
171s Unpacking libpaper1:arm64 (1.1.29) ...
171s Selecting previously unselected package libpaper-utils.
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171s Unpacking libpaper-utils (1.1.29) ...
171s Selecting previously unselected package libsharpyuv0:arm64.
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171s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
171s Selecting previously unselected package libsm6:arm64.
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171s Unpacking libsm6:arm64 (2:1.2.3-1build2) ...
171s Selecting previously unselected package libtcl8.6:arm64.
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172s Selecting previously unselected package libjbig0:arm64.
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172s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
172s Selecting previously unselected package libwebp7:arm64.
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172s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
172s Selecting previously unselected package libtiff6:arm64.
172s Preparing to unpack .../37-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
172s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
172s Selecting previously unselected package libxft2:arm64.
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172s Unpacking libxft2:arm64 (2.3.6-1) ...
172s Selecting previously unselected package libxss1:arm64.
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172s Unpacking libxss1:arm64 (1:1.2.3-1build2) ...
172s Selecting previously unselected package libtk8.6:arm64.
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172s Unpacking libtk8.6:arm64 (8.6.13-2) ...
172s Selecting previously unselected package libxt6:arm64.
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172s Unpacking libxt6:arm64 (1:1.2.1-1.1) ...
172s Selecting previously unselected package zip.
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172s Unpacking zip (3.0-13) ...
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172s Unpacking unzip (6.0-28ubuntu3) ...
172s Selecting previously unselected package xdg-utils.
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172s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
172s Selecting previously unselected package r-base-core.
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172s Unpacking r-base-core (4.3.2-1build1) ...
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174s Unpacking bowtie (1.3.1-3) ...
174s Selecting previously unselected package rsem.
174s Preparing to unpack .../47-rsem_1.3.3+dfsg-3_arm64.deb ...
174s Unpacking rsem (1.3.3+dfsg-3) ...
174s Selecting previously unselected package autopkgtest-satdep.
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174s Unpacking autopkgtest-satdep (0) ...
174s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
174s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
174s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
174s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
174s Setting up libpaper1:arm64 (1.1.29) ...
175s 
175s Creating config file /etc/papersize with new version
175s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
175s Setting up bowtie (1.3.1-3) ...
175s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
175s Setting up libdatrie1:arm64 (0.2.13-3) ...
175s Setting up libxcb-render0:arm64 (1.15-1) ...
175s Setting up unzip (6.0-28ubuntu3) ...
175s Setting up x11-common (1:7.7+23ubuntu2) ...
176s Setting up libdeflate0:arm64 (1.19-1) ...
176s Setting up libxcb-shm0:arm64 (1.15-1) ...
176s Setting up libpaper-utils (1.1.29) ...
176s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
176s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
176s Setting up zip (3.0-13) ...
176s Setting up libblas3:arm64 (3.12.0-3) ...
176s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
176s Setting up fonts-dejavu-mono (2.37-8) ...
176s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ...
176s Setting up fonts-dejavu-core (2.37-8) ...
176s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
176s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
176s Setting up libwebp7:arm64 (1.3.2-0.4) ...
176s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
176s Setting up libthai-data (0.1.29-2) ...
176s Setting up libxss1:arm64 (1:1.2.3-1build2) ...
176s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
176s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
176s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
176s Setting up libice6:arm64 (2:1.0.10-1build2) ...
176s Setting up liblapack3:arm64 (3.12.0-3) ...
176s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
176s Setting up libhts3:arm64 (1.19+ds-1) ...
176s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
177s Setting up libthai0:arm64 (0.1.29-2) ...
177s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
177s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
177s Setting up libsm6:arm64 (2:1.2.3-1build2) ...
177s Setting up fontconfig (2.15.0-1ubuntu1) ...
179s Regenerating fonts cache... done.
179s Setting up libxft2:arm64 (2.3.6-1) ...
179s Setting up libtk8.6:arm64 (8.6.13-2) ...
179s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
179s Setting up libcairo2:arm64 (1.18.0-1) ...
179s Setting up libxt6:arm64 (1:1.2.1-1.1) ...
179s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
179s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
179s Setting up r-base-core (4.3.2-1build1) ...
179s 
179s Creating config file /etc/R/Renviron with new version
179s Setting up rsem (1.3.3+dfsg-3) ...
179s Setting up autopkgtest-satdep (0) ...
179s Processing triggers for man-db (2.12.0-3) ...
181s Processing triggers for install-info (7.1-3) ...
181s Processing triggers for libc-bin (2.39-0ubuntu2) ...
189s (Reading database ... 77956 files and directories currently installed.)
189s Removing autopkgtest-satdep (0) ...
189s autopkgtest [17:17:49]: test run-unit-test: [-----------------------
190s + pkg=rsem
190s + '[' /tmp/autopkgtest.ilYrHy/autopkgtest_tmp = '' ']'
190s + cp -a /usr/share/doc/rsem/examples/mouse_ref_building_from_transcripts.tar.gz /tmp/autopkgtest.ilYrHy/autopkgtest_tmp
190s + cd /tmp/autopkgtest.ilYrHy/autopkgtest_tmp
190s + tar -C . -xzf mouse_ref_building_from_transcripts.tar.gz
192s + rsem-prepare-reference --transcript-to-gene-map mouse_ref_mapping.txt mouse_ref.fa mouse_ref
193s rsem-synthesis-reference-transcripts mouse_ref 0 1 mouse_ref_mapping.txt mouse_ref.fa
204s Transcript Information File is generated!
204s Group File is generated!
204s Extracted Sequences File is generated!
204s 
204s rsem-preref mouse_ref.transcripts.fa 1 mouse_ref
214s Refs.makeRefs finished!
214s Refs.saveRefs finished!
214s mouse_ref.idx.fa is generated!
214s mouse_ref.n2g.idx.fa is generated!
215s 
215s autopkgtest [17:18:15]: test run-unit-test: -----------------------]
215s run-unit-test        PASS
215s autopkgtest [17:18:15]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
216s autopkgtest [17:18:16]: @@@@@@@@@@@@@@@@@@@@ summary
216s run-unit-test        PASS
228s Creating nova instance adt-noble-arm64-rsem-20240316-171440-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240316.img (UUID 9d2e92bf-2787-45c2-ae22-99fb4bcc175e)...