0s autopkgtest [21:20:17]: starting date and time: 2024-03-16 21:20:17+0000
  0s autopkgtest [21:20:17]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [21:20:17]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5xmn2pw8/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base,src:curl,src:glib2.0,src:libpng1.6,src:libpsl,src:libtirpc,src:libxt,src:openssl,src:orthanc-python,src:readline,src:wp2latex --apt-upgrade rsem --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 curl/8.5.0-2ubuntu7 glib2.0/2.79.3-3ubuntu5 libpng1.6/1.6.43-3 libpsl/0.21.2-1.1 libtirpc/1.3.4+ds-1.1 libxt/1:1.2.1-1.2 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 readline/8.2-3.1 wp2latex/4.4~ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-20.secgroup --name adt-noble-arm64-rsem-20240316-212016-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/
105s autopkgtest [21:22:02]: testbed dpkg architecture: arm64
105s autopkgtest [21:22:02]: testbed apt version: 2.7.12
105s autopkgtest [21:22:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup
105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB]
106s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3703 kB]
106s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
106s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
106s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
106s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
106s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
106s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4017 kB]
106s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
106s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.5 kB]
106s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
108s Fetched 9115 kB in 2s (4889 kB/s)
108s Reading package lists...
111s Reading package lists...
111s Building dependency tree...
111s Reading state information...
111s Calculating upgrade...
112s The following packages will be REMOVED:
112s   libglib2.0-0 libssl3
112s The following NEW packages will be installed:
112s   libglib2.0-0t64 libssl3t64 xdg-user-dirs
112s The following packages have been kept back:
112s   curl
112s The following packages will be upgraded:
112s   gir1.2-glib-2.0 libglib2.0-data libtirpc-common openssl readline-common
112s   ubuntu-minimal ubuntu-standard
112s 7 upgraded, 3 newly installed, 2 to remove and 1 not upgraded.
112s Need to get 4613 kB of archives.
112s After this operation, 211 kB of additional disk space will be used.
112s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gir1.2-glib-2.0 arm64 2.79.3-3ubuntu5 [182 kB]
112s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-0t64 arm64 2.79.3-3ubuntu5 [1527 kB]
112s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
112s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
113s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libglib2.0-data all 2.79.3-3ubuntu5 [46.6 kB]
113s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1 [8018 B]
113s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-3.1 [56.4 kB]
113s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
113s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-user-dirs arm64 0.18-1 [18.1 kB]
113s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
113s Fetched 4613 kB in 1s (6030 kB/s)
113s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
113s Preparing to unpack .../gir1.2-glib-2.0_2.79.3-3ubuntu5_arm64.deb ...
113s Unpacking gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
113s dpkg: libglib2.0-0:arm64: dependency problems, but removing anyway as you requested:
113s  udisks2 depends on libglib2.0-0 (>= 2.77.0).
113s  shared-mime-info depends on libglib2.0-0 (>= 2.75.3).
113s  python3-gi depends on libglib2.0-0 (>= 2.77.0).
113s  python3-dbus depends on libglib2.0-0 (>= 2.16.0).
113s  netplan.io depends on libglib2.0-0 (>= 2.70.0).
113s  netplan-generator depends on libglib2.0-0 (>= 2.70.0).
113s  libxmlb2:arm64 depends on libglib2.0-0 (>= 2.54.0).
113s  libvolume-key1:arm64 depends on libglib2.0-0 (>= 2.18.0).
113s  libudisks2-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
113s  libqrtr-glib0:arm64 depends on libglib2.0-0 (>= 2.56).
113s  libqmi-proxy depends on libglib2.0-0 (>= 2.30.0).
113s  libqmi-glib5:arm64 depends on libglib2.0-0 (>= 2.54.0).
113s  libpolkit-gobject-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
113s  libpolkit-agent-1-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
113s  libnetplan0:arm64 depends on libglib2.0-0 (>= 2.75.3).
113s  libmm-glib0:arm64 depends on libglib2.0-0 (>= 2.62.0).
113s  libmbim-proxy depends on libglib2.0-0 (>= 2.56).
113s  libmbim-glib4:arm64 depends on libglib2.0-0 (>= 2.56).
113s  libjson-glib-1.0-0:arm64 depends on libglib2.0-0 (>= 2.75.3).
113s  libjcat1:arm64 depends on libglib2.0-0 (>= 2.75.3).
113s  libgusb2:arm64 depends on libglib2.0-0 (>= 2.75.3).
113s  libgudev-1.0-0:arm64 depends on libglib2.0-0 (>= 2.38.0).
113s  libgirepository-1.0-1:arm64 depends on libglib2.0-0 (>= 2.79.0).
113s  libfwupd2:arm64 depends on libglib2.0-0 (>= 2.79.0).
113s  libblockdev3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-utils3:arm64 depends on libglib2.0-0 (>= 2.75.3).
113s  libblockdev-swap3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-part3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-nvme3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-mdraid3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-loop3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-fs3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  libblockdev-crypto3:arm64 depends on libglib2.0-0 (>= 2.42.2).
113s  fwupd depends on libglib2.0-0 (>= 2.79.0).
113s  bolt depends on libglib2.0-0 (>= 2.56.0).
113s 
113s (Reading database ... 
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113s Removing libglib2.0-0:arm64 (2.79.2-1~ubuntu1) ...
113s Selecting previously unselected package libglib2.0-0t64:arm64.
113s (Reading database ... 
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113s Preparing to unpack .../libglib2.0-0t64_2.79.3-3ubuntu5_arm64.deb ...
113s libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:arm64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled...
113s removed '/var/lib/dpkg/info/libglib2.0-0:arm64.postrm'
113s Unpacking libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
114s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
114s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
114s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
114s  wget depends on libssl3 (>= 3.0.0).
114s  u-boot-tools depends on libssl3 (>= 3.0.0).
114s  tnftp depends on libssl3 (>= 3.0.0).
114s  tcpdump depends on libssl3 (>= 3.0.0).
114s  systemd-resolved depends on libssl3 (>= 3.0.0).
114s  systemd depends on libssl3 (>= 3.0.0).
114s  sudo depends on libssl3 (>= 3.0.0).
114s  sbsigntool depends on libssl3 (>= 3.0.0).
114s  rsync depends on libssl3 (>= 3.0.0).
114s  python3-cryptography depends on libssl3 (>= 3.0.0).
114s  openssh-server depends on libssl3 (>= 3.0.10).
114s  openssh-client depends on libssl3 (>= 3.0.10).
114s  mtd-utils depends on libssl3 (>= 3.0.0).
114s  mokutil depends on libssl3 (>= 3.0.0).
114s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
114s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
114s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
114s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
114s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
114s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
114s  libnvme1 depends on libssl3 (>= 3.0.0).
114s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
114s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
114s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
114s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
114s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
114s  kmod depends on libssl3 (>= 3.0.0).
114s  dhcpcd-base depends on libssl3 (>= 3.0.0).
114s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
114s 
114s (Reading database ... 
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114s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
114s Selecting previously unselected package libssl3t64:arm64.
114s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
114s Preparing to unpack .../0-libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
114s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
114s Preparing to unpack .../1-libglib2.0-data_2.79.3-3ubuntu5_all.deb ...
114s Unpacking libglib2.0-data (2.79.3-3ubuntu5) over (2.79.2-1~ubuntu1) ...
114s Preparing to unpack .../2-libtirpc-common_1.3.4+ds-1.1_all.deb ...
114s Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1build1) ...
114s Preparing to unpack .../3-readline-common_8.2-3.1_all.deb ...
114s Unpacking readline-common (8.2-3.1) over (8.2-3) ...
114s Preparing to unpack .../4-ubuntu-minimal_1.536_arm64.deb ...
114s Unpacking ubuntu-minimal (1.536) over (1.535) ...
114s Selecting previously unselected package xdg-user-dirs.
114s Preparing to unpack .../5-xdg-user-dirs_0.18-1_arm64.deb ...
114s Unpacking xdg-user-dirs (0.18-1) ...
114s Preparing to unpack .../6-ubuntu-standard_1.536_arm64.deb ...
114s Unpacking ubuntu-standard (1.536) over (1.535) ...
114s Setting up ubuntu-minimal (1.536) ...
114s Setting up xdg-user-dirs (0.18-1) ...
114s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
114s Setting up libtirpc-common (1.3.4+ds-1.1) ...
114s Setting up ubuntu-standard (1.536) ...
114s Setting up libglib2.0-0t64:arm64 (2.79.3-3ubuntu5) ...
114s No schema files found: doing nothing.
114s Setting up libglib2.0-data (2.79.3-3ubuntu5) ...
114s Setting up gir1.2-glib-2.0:arm64 (2.79.3-3ubuntu5) ...
114s Setting up openssl (3.0.13-0ubuntu1) ...
114s Setting up readline-common (8.2-3.1) ...
114s Processing triggers for man-db (2.12.0-3) ...
115s Processing triggers for install-info (7.1-3) ...
115s Processing triggers for libc-bin (2.39-0ubuntu2) ...
115s Reading package lists...
116s Building dependency tree...
116s Reading state information...
116s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
117s sh: Attempting to set up Debian/Ubuntu apt sources automatically
117s sh: Distribution appears to be Ubuntu
117s Reading package lists...
118s Building dependency tree...
118s Reading state information...
118s eatmydata is already the newest version (131-1).
118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
118s Reading package lists...
118s Building dependency tree...
118s Reading state information...
119s dbus is already the newest version (1.14.10-4ubuntu1).
119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
120s rng-tools-debian is already the newest version (2.4).
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s Reading package lists...
120s Building dependency tree...
120s Reading state information...
121s The following packages will be REMOVED:
121s   cloud-init* python3-configobj* python3-debconf*
121s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
121s After this operation, 3252 kB disk space will be freed.
121s (Reading database ... 
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(Reading database ... 74774 files and directories currently installed.)
121s Removing cloud-init (24.1.1-0ubuntu1) ...
121s Removing python3-configobj (5.0.8-3) ...
121s Removing python3-debconf (1.5.86) ...
122s Processing triggers for man-db (2.12.0-3) ...
122s (Reading database ... 
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(Reading database ... 74385 files and directories currently installed.)
122s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ...
122s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
122s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
122s invoke-rc.d: policy-rc.d denied execution of try-restart.
123s Reading package lists...
123s Building dependency tree...
123s Reading state information...
124s linux-generic is already the newest version (6.8.0-11.11+1).
124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
124s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
124s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
124s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
126s Reading package lists...
126s Reading package lists...
126s Building dependency tree...
126s Reading state information...
127s Calculating upgrade...
127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
127s Reading package lists...
127s Building dependency tree...
127s Reading state information...
128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s autopkgtest [21:22:25]: rebooting testbed after setup commands that affected boot
300s autopkgtest [21:25:17]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
302s autopkgtest [21:25:19]: @@@@@@@@@@@@@@@@@@@@ apt-source rsem
305s Get:1 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (dsc) [2249 B]
305s Get:2 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (tar) [275 kB]
305s Get:3 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (diff) [35.7 MB]
306s gpgv: Signature made Mon Dec 18 13:04:45 2023 UTC
306s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
306s gpgv:                issuer "emollier@debian.org"
306s gpgv: Can't check signature: No public key
306s dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found
306s autopkgtest [21:25:23]: testing package rsem version 1.3.3+dfsg-3
308s autopkgtest [21:25:25]: build not needed
309s autopkgtest [21:25:26]: test run-unit-test: preparing testbed
310s Reading package lists...
311s Building dependency tree...
311s Reading state information...
311s Starting pkgProblemResolver with broken count: 0
311s Starting 2 pkgProblemResolver with broken count: 0
311s Done
311s The following additional packages will be installed:
311s   bowtie fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
311s   libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5
311s   libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0
311s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
311s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
311s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
311s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
311s   r-base-core rsem unzip x11-common xdg-utils zip
311s Suggested packages:
311s   bowtie-examples tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib
311s   r-base-html r-bioc-ebseq hisat2
311s Recommended packages:
311s   r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl
311s   libx11-protocol-perl x11-utils x11-xserver-utils
312s The following NEW packages will be installed:
312s   autopkgtest-satdep bowtie fontconfig fontconfig-config fonts-dejavu-core
312s   fonts-dejavu-mono libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1
312s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2
312s   libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
312s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
312s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
312s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
312s   r-base-core rsem unzip x11-common xdg-utils zip
312s 0 upgraded, 49 newly installed, 0 to remove and 0 not upgraded.
312s Need to get 74.5 MB/74.5 MB of archives.
312s After this operation, 120 MB of additional disk space will be used.
312s Get:1 /tmp/autopkgtest.7KuhiH/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B]
312s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
312s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
312s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
312s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
312s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
312s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
312s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
313s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
313s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
313s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
313s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
313s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
313s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
313s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
313s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
313s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
313s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
313s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
313s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
313s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
313s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB]
313s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
313s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
313s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
313s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
313s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
313s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
313s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
313s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
313s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
313s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB]
313s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B]
313s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
313s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB]
313s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
313s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
313s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
313s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
313s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
313s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
313s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
313s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB]
313s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB]
313s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB]
313s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
313s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB]
315s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie arm64 1.3.1-3 [1346 kB]
315s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 rsem arm64 1.3.3+dfsg-3 [36.0 MB]
317s Preconfiguring packages ...
317s Fetched 74.5 MB in 4s (17.0 MB/s)
317s Selecting previously unselected package fonts-dejavu-mono.
317s (Reading database ... 
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(Reading database ... 74330 files and directories currently installed.)
317s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ...
317s Unpacking fonts-dejavu-mono (2.37-8) ...
317s Selecting previously unselected package fonts-dejavu-core.
317s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ...
317s Unpacking fonts-dejavu-core (2.37-8) ...
317s Selecting previously unselected package fontconfig-config.
317s Preparing to unpack .../02-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
317s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
317s Selecting previously unselected package libfontconfig1:arm64.
317s Preparing to unpack .../03-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
317s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
317s Selecting previously unselected package fontconfig.
317s Preparing to unpack .../04-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
317s Unpacking fontconfig (2.15.0-1ubuntu1) ...
317s Selecting previously unselected package libblas3:arm64.
317s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ...
317s Unpacking libblas3:arm64 (3.12.0-3) ...
317s Selecting previously unselected package libpixman-1-0:arm64.
317s Preparing to unpack .../06-libpixman-1-0_0.42.2-1_arm64.deb ...
317s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
317s Selecting previously unselected package libxcb-render0:arm64.
317s Preparing to unpack .../07-libxcb-render0_1.15-1_arm64.deb ...
317s Unpacking libxcb-render0:arm64 (1.15-1) ...
317s Selecting previously unselected package libxcb-shm0:arm64.
317s Preparing to unpack .../08-libxcb-shm0_1.15-1_arm64.deb ...
317s Unpacking libxcb-shm0:arm64 (1.15-1) ...
317s Selecting previously unselected package libxrender1:arm64.
317s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
317s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
317s Selecting previously unselected package libcairo2:arm64.
317s Preparing to unpack .../10-libcairo2_1.18.0-1_arm64.deb ...
317s Unpacking libcairo2:arm64 (1.18.0-1) ...
317s Selecting previously unselected package libdatrie1:arm64.
317s Preparing to unpack .../11-libdatrie1_0.2.13-3_arm64.deb ...
317s Unpacking libdatrie1:arm64 (0.2.13-3) ...
317s Selecting previously unselected package libdeflate0:arm64.
317s Preparing to unpack .../12-libdeflate0_1.19-1_arm64.deb ...
317s Unpacking libdeflate0:arm64 (1.19-1) ...
317s Selecting previously unselected package libgfortran5:arm64.
317s Preparing to unpack .../13-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
317s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
317s Selecting previously unselected package libgomp1:arm64.
318s Preparing to unpack .../14-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
318s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
318s Selecting previously unselected package libgraphite2-3:arm64.
318s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_arm64.deb ...
318s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
318s Selecting previously unselected package libharfbuzz0b:arm64.
318s Preparing to unpack .../16-libharfbuzz0b_8.3.0-2_arm64.deb ...
318s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
318s Selecting previously unselected package libhtscodecs2:arm64.
318s Preparing to unpack .../17-libhtscodecs2_1.6.0-1_arm64.deb ...
318s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
318s Selecting previously unselected package libhts3:arm64.
318s Preparing to unpack .../18-libhts3_1.18+ds-1_arm64.deb ...
318s Unpacking libhts3:arm64 (1.18+ds-1) ...
318s Selecting previously unselected package x11-common.
318s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu2_all.deb ...
318s Unpacking x11-common (1:7.7+23ubuntu2) ...
318s Selecting previously unselected package libice6:arm64.
318s Preparing to unpack .../20-libice6_2%3a1.0.10-1build2_arm64.deb ...
318s Unpacking libice6:arm64 (2:1.0.10-1build2) ...
318s Selecting previously unselected package libjpeg-turbo8:arm64.
318s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
318s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
318s Selecting previously unselected package libjpeg8:arm64.
318s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ...
318s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
318s Selecting previously unselected package liblapack3:arm64.
318s Preparing to unpack .../23-liblapack3_3.12.0-3_arm64.deb ...
318s Unpacking liblapack3:arm64 (3.12.0-3) ...
318s Selecting previously unselected package liblerc4:arm64.
318s Preparing to unpack .../24-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
318s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
318s Selecting previously unselected package libthai-data.
318s Preparing to unpack .../25-libthai-data_0.1.29-2_all.deb ...
318s Unpacking libthai-data (0.1.29-2) ...
318s Selecting previously unselected package libthai0:arm64.
318s Preparing to unpack .../26-libthai0_0.1.29-2_arm64.deb ...
318s Unpacking libthai0:arm64 (0.1.29-2) ...
318s Selecting previously unselected package libpango-1.0-0:arm64.
318s Preparing to unpack .../27-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
318s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
318s Selecting previously unselected package libpangoft2-1.0-0:arm64.
318s Preparing to unpack .../28-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ...
318s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
318s Selecting previously unselected package libpangocairo-1.0-0:arm64.
318s Preparing to unpack .../29-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ...
318s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
318s Selecting previously unselected package libpaper1:arm64.
318s Preparing to unpack .../30-libpaper1_1.1.29_arm64.deb ...
318s Unpacking libpaper1:arm64 (1.1.29) ...
318s Selecting previously unselected package libpaper-utils.
318s Preparing to unpack .../31-libpaper-utils_1.1.29_arm64.deb ...
318s Unpacking libpaper-utils (1.1.29) ...
318s Selecting previously unselected package libsharpyuv0:arm64.
318s Preparing to unpack .../32-libsharpyuv0_1.3.2-0.4_arm64.deb ...
318s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
318s Selecting previously unselected package libsm6:arm64.
318s Preparing to unpack .../33-libsm6_2%3a1.2.3-1build2_arm64.deb ...
318s Unpacking libsm6:arm64 (2:1.2.3-1build2) ...
318s Selecting previously unselected package libtcl8.6:arm64.
318s Preparing to unpack .../34-libtcl8.6_8.6.13+dfsg-2_arm64.deb ...
318s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ...
318s Selecting previously unselected package libjbig0:arm64.
318s Preparing to unpack .../35-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
318s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
318s Selecting previously unselected package libwebp7:arm64.
319s Preparing to unpack .../36-libwebp7_1.3.2-0.4_arm64.deb ...
319s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
319s Selecting previously unselected package libtiff6:arm64.
319s Preparing to unpack .../37-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
319s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
319s Selecting previously unselected package libxft2:arm64.
319s Preparing to unpack .../38-libxft2_2.3.6-1_arm64.deb ...
319s Unpacking libxft2:arm64 (2.3.6-1) ...
319s Selecting previously unselected package libxss1:arm64.
319s Preparing to unpack .../39-libxss1_1%3a1.2.3-1build2_arm64.deb ...
319s Unpacking libxss1:arm64 (1:1.2.3-1build2) ...
319s Selecting previously unselected package libtk8.6:arm64.
319s Preparing to unpack .../40-libtk8.6_8.6.13-2_arm64.deb ...
319s Unpacking libtk8.6:arm64 (8.6.13-2) ...
319s Selecting previously unselected package libxt6:arm64.
319s Preparing to unpack .../41-libxt6_1%3a1.2.1-1.1_arm64.deb ...
319s Unpacking libxt6:arm64 (1:1.2.1-1.1) ...
319s Selecting previously unselected package zip.
319s Preparing to unpack .../42-zip_3.0-13_arm64.deb ...
319s Unpacking zip (3.0-13) ...
319s Selecting previously unselected package unzip.
319s Preparing to unpack .../43-unzip_6.0-28ubuntu3_arm64.deb ...
319s Unpacking unzip (6.0-28ubuntu3) ...
319s Selecting previously unselected package xdg-utils.
319s Preparing to unpack .../44-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
319s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
319s Selecting previously unselected package r-base-core.
319s Preparing to unpack .../45-r-base-core_4.3.2-1build1_arm64.deb ...
319s Unpacking r-base-core (4.3.2-1build1) ...
319s Selecting previously unselected package bowtie.
319s Preparing to unpack .../46-bowtie_1.3.1-3_arm64.deb ...
319s Unpacking bowtie (1.3.1-3) ...
319s Selecting previously unselected package rsem.
319s Preparing to unpack .../47-rsem_1.3.3+dfsg-3_arm64.deb ...
319s Unpacking rsem (1.3.3+dfsg-3) ...
319s Selecting previously unselected package autopkgtest-satdep.
319s Preparing to unpack .../48-1-autopkgtest-satdep.deb ...
319s Unpacking autopkgtest-satdep (0) ...
319s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
319s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
319s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
319s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
319s Setting up libpaper1:arm64 (1.1.29) ...
320s 
320s Creating config file /etc/papersize with new version
320s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
320s Setting up bowtie (1.3.1-3) ...
320s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
320s Setting up libdatrie1:arm64 (0.2.13-3) ...
320s Setting up libxcb-render0:arm64 (1.15-1) ...
320s Setting up unzip (6.0-28ubuntu3) ...
320s Setting up x11-common (1:7.7+23ubuntu2) ...
320s Setting up libdeflate0:arm64 (1.19-1) ...
320s Setting up libxcb-shm0:arm64 (1.15-1) ...
320s Setting up libpaper-utils (1.1.29) ...
320s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
320s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
320s Setting up zip (3.0-13) ...
320s Setting up libblas3:arm64 (3.12.0-3) ...
320s 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
320s Setting up fonts-dejavu-mono (2.37-8) ...
320s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ...
320s Setting up fonts-dejavu-core (2.37-8) ...
320s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
320s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
320s Setting up libwebp7:arm64 (1.3.2-0.4) ...
320s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
320s Setting up libthai-data (0.1.29-2) ...
320s Setting up libxss1:arm64 (1:1.2.3-1build2) ...
320s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
320s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
320s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
320s Setting up libice6:arm64 (2:1.0.10-1build2) ...
320s Setting up liblapack3:arm64 (3.12.0-3) ...
320s 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
320s Setting up libhts3:arm64 (1.18+ds-1) ...
320s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
321s Setting up libthai0:arm64 (0.1.29-2) ...
321s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
321s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
321s Setting up libsm6:arm64 (2:1.2.3-1build2) ...
321s Setting up fontconfig (2.15.0-1ubuntu1) ...
323s Regenerating fonts cache... done.
323s Setting up libxft2:arm64 (2.3.6-1) ...
323s Setting up libtk8.6:arm64 (8.6.13-2) ...
323s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
323s Setting up libcairo2:arm64 (1.18.0-1) ...
323s Setting up libxt6:arm64 (1:1.2.1-1.1) ...
323s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
323s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
323s Setting up r-base-core (4.3.2-1build1) ...
323s 
323s Creating config file /etc/R/Renviron with new version
323s Setting up rsem (1.3.3+dfsg-3) ...
323s Setting up autopkgtest-satdep (0) ...
323s Processing triggers for man-db (2.12.0-3) ...
324s Processing triggers for install-info (7.1-3) ...
324s Processing triggers for libc-bin (2.39-0ubuntu2) ...
328s (Reading database ... 76434 files and directories currently installed.)
328s Removing autopkgtest-satdep (0) ...
328s autopkgtest [21:25:45]: test run-unit-test: [-----------------------
329s + pkg=rsem
329s + '[' /tmp/autopkgtest.7KuhiH/autopkgtest_tmp = '' ']'
329s + cp -a /usr/share/doc/rsem/examples/mouse_ref_building_from_transcripts.tar.gz /tmp/autopkgtest.7KuhiH/autopkgtest_tmp
329s + cd /tmp/autopkgtest.7KuhiH/autopkgtest_tmp
329s + tar -C . -xzf mouse_ref_building_from_transcripts.tar.gz
330s + rsem-prepare-reference --transcript-to-gene-map mouse_ref_mapping.txt mouse_ref.fa mouse_ref
330s rsem-synthesis-reference-transcripts mouse_ref 0 1 mouse_ref_mapping.txt mouse_ref.fa
334s Transcript Information File is generated!
334s Group File is generated!
334s Extracted Sequences File is generated!
334s 
334s rsem-preref mouse_ref.transcripts.fa 1 mouse_ref
337s Refs.makeRefs finished!
337s Refs.saveRefs finished!
337s mouse_ref.idx.fa is generated!
337s mouse_ref.n2g.idx.fa is generated!
337s 
338s autopkgtest [21:25:55]: test run-unit-test: -----------------------]
338s autopkgtest [21:25:55]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
338s run-unit-test        PASS
338s autopkgtest [21:25:55]: @@@@@@@@@@@@@@@@@@@@ summary
338s run-unit-test        PASS
342s Creating nova instance adt-noble-arm64-rsem-20240316-212016-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...