0s autopkgtest [03:48:11]: starting date: 2024-03-11
  0s autopkgtest [03:48:11]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline
  0s autopkgtest [03:48:11]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.38hc66ui/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:perl,src:db5.3,src:gdbm,src:mmdebstrap --apt-upgrade rsem --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 db5.3/5.3.28+dfsg2-5 gdbm/1.23-5.1 mmdebstrap/1.4.3-6' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-7.secgroup --name adt-noble-arm64-rsem-20240311-034810-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/
145s autopkgtest [03:50:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup
146s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
146s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B]
146s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [37.3 kB]
146s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2615 kB]
147s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [434 kB]
147s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [581 kB]
147s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
147s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB]
147s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
147s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2990 kB]
147s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
147s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [39.6 kB]
147s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
148s Fetched 6850 kB in 1s (4608 kB/s)
149s Reading package lists...
151s Reading package lists...
152s Building dependency tree...
152s Reading state information...
152s Calculating upgrade...
153s The following packages were automatically installed and are no longer required:
153s   libgdbm-compat4t64 libperl5.38 lto-disabled-list make perl-modules-5.38
153s Use 'sudo apt autoremove' to remove them.
153s The following packages will be REMOVED:
153s   dpkg-dev libdpkg-perl libgdbm-compat4 libgdbm6 perl
153s The following NEW packages will be installed:
153s   libgdbm-compat4t64 libgdbm6t64
153s The following packages have been kept back:
153s   libperl5.38
153s The following packages will be upgraded:
153s   perl-base perl-modules-5.38
155s 2 upgraded, 2 newly installed, 5 to remove and 1 not upgraded.
155s Need to get 4928 kB of archives.
155s After this operation, 4158 kB disk space will be freed.
155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2 [1777 kB]
156s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1 [34.3 kB]
156s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1 [6576 B]
156s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB]
157s Fetched 4928 kB in 2s (1989 kB/s)
157s (Reading database ... 
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157s Removing dpkg-dev (1.22.4ubuntu5) ...
157s Removing libdpkg-perl (1.22.4ubuntu5) ...
157s Removing perl (5.38.2-3) ...
158s (Reading database ... 
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158s Preparing to unpack .../perl-base_5.38.2-3.2_arm64.deb ...
158s Unpacking perl-base (5.38.2-3.2) over (5.38.2-3) ...
158s Setting up perl-base (5.38.2-3.2) ...
158s dpkg: libgdbm6:arm64: dependency problems, but removing anyway as you requested:
158s  python3-gdbm:arm64 depends on libgdbm6 (>= 1.16).
158s  man-db depends on libgdbm6 (>= 1.16).
158s  libperl5.38:arm64 depends on libgdbm6 (>= 1.21).
158s  libgdbm-compat4:arm64 depends on libgdbm6 (>= 1.16).
158s 
158s (Reading database ... 
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(Reading database ... 74167 files and directories currently installed.)
158s Removing libgdbm6:arm64 (1.23-5) ...
158s Selecting previously unselected package libgdbm6t64:arm64.
158s (Reading database ... 
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(Reading database ... 74162 files and directories currently installed.)
158s Preparing to unpack .../libgdbm6t64_1.23-5.1_arm64.deb ...
158s Unpacking libgdbm6t64:arm64 (1.23-5.1) ...
158s dpkg: libgdbm-compat4:arm64: dependency problems, but removing anyway as you requested:
158s  libperl5.38:arm64 depends on libgdbm-compat4 (>= 1.18-3).
158s 
158s (Reading database ... 
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158s Removing libgdbm-compat4:arm64 (1.23-5) ...
158s Selecting previously unselected package libgdbm-compat4t64:arm64.
158s (Reading database ... 
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(Reading database ... 74163 files and directories currently installed.)
158s Preparing to unpack .../libgdbm-compat4t64_1.23-5.1_arm64.deb ...
158s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
158s Preparing to unpack .../perl-modules-5.38_5.38.2-3.2_all.deb ...
158s Unpacking perl-modules-5.38 (5.38.2-3.2) over (5.38.2-3) ...
159s Setting up libgdbm6t64:arm64 (1.23-5.1) ...
159s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
159s Setting up perl-modules-5.38 (5.38.2-3.2) ...
159s Processing triggers for man-db (2.12.0-3) ...
161s Processing triggers for libc-bin (2.39-0ubuntu2) ...
161s Reading package lists...
162s Building dependency tree...
162s Reading state information...
162s The following packages will be REMOVED:
162s   libgdbm-compat4t64* libperl5.38* lto-disabled-list* make* perl-modules-5.38*
163s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded.
163s After this operation, 52.0 MB disk space will be freed.
163s (Reading database ... 
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163s Removing libperl5.38:arm64 (5.38.2-3) ...
163s Removing libgdbm-compat4t64:arm64 (1.23-5.1) ...
163s Removing lto-disabled-list (47) ...
163s Removing make (4.3-4.1build1) ...
163s Removing perl-modules-5.38 (5.38.2-3.2) ...
163s Processing triggers for man-db (2.12.0-3) ...
163s Processing triggers for libc-bin (2.39-0ubuntu2) ...
166s sh: Attempting to set up Debian/Ubuntu apt sources automatically
166s sh: Distribution appears to be Ubuntu
167s Reading package lists...
167s Building dependency tree...
167s Reading state information...
168s eatmydata is already the newest version (131-1).
168s dbus is already the newest version (1.14.10-4ubuntu1).
168s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
168s Reading package lists...
168s Building dependency tree...
168s Reading state information...
168s rng-tools-debian is already the newest version (2.4).
168s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
169s Reading package lists...
169s Building dependency tree...
169s Reading state information...
169s haveged is already the newest version (1.9.14-1ubuntu1).
169s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
169s Reading package lists...
170s Building dependency tree...
170s Reading state information...
170s The following additional packages will be installed:
170s   libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64 lto-disabled-list
170s   make perl perl-modules-5.38
170s Suggested packages:
170s   debian-keyring gcc | c-compiler git bzr make-doc perl-doc
170s   libterm-readline-gnu-perl | libterm-readline-perl-perl
170s   libtap-harness-archive-perl
170s Recommended packages:
170s   build-essential gcc | c-compiler fakeroot libalgorithm-merge-perl
170s   libfile-fcntllock-perl
170s The following packages will be REMOVED:
170s   libdb5.3
170s The following NEW packages will be installed:
170s   dpkg-dev libdb5.3t64 libdpkg-perl libgdbm-compat4t64 libperl5.38t64
170s   lto-disabled-list make perl perl-modules-5.38
171s 0 upgraded, 9 newly installed, 1 to remove and 0 not upgraded.
171s Need to get 7257 kB/10.4 MB of archives.
171s After this operation, 56.1 MB of additional disk space will be used.
171s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-5 [719 kB]
171s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2 [4771 kB]
171s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2 [231 kB]
171s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.4ubuntu5 [268 kB]
171s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 make arm64 4.3-4.1build1 [177 kB]
171s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB]
171s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.4ubuntu5 [1078 kB]
172s Fetched 7257 kB in 1s (8822 kB/s)
172s dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested:
172s  libsasl2-modules-db:arm64 depends on libdb5.3.
172s  libpython3.12-stdlib:arm64 depends on libdb5.3.
172s  libpam-modules:arm64 depends on libdb5.3.
172s  iproute2 depends on libdb5.3.
172s  apt-utils depends on libdb5.3.
172s 
172s (Reading database ... 
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172s Removing libdb5.3:arm64 (5.3.28+dfsg2-4) ...
172s Selecting previously unselected package libdb5.3t64:arm64.
172s (Reading database ... 
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172s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_arm64.deb ...
172s Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-5) ...
172s Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-5) ...
173s Selecting previously unselected package perl-modules-5.38.
173s (Reading database ... 
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173s Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ...
173s Unpacking perl-modules-5.38 (5.38.2-3.2) ...
173s Selecting previously unselected package libgdbm-compat4t64:arm64.
173s Preparing to unpack .../1-libgdbm-compat4t64_1.23-5.1_arm64.deb ...
173s Unpacking libgdbm-compat4t64:arm64 (1.23-5.1) ...
173s Selecting previously unselected package libperl5.38t64:arm64.
173s Preparing to unpack .../2-libperl5.38t64_5.38.2-3.2_arm64.deb ...
173s Unpacking libperl5.38t64:arm64 (5.38.2-3.2) ...
174s Selecting previously unselected package perl.
174s Preparing to unpack .../3-perl_5.38.2-3.2_arm64.deb ...
174s Unpacking perl (5.38.2-3.2) ...
174s Selecting previously unselected package libdpkg-perl.
174s Preparing to unpack .../4-libdpkg-perl_1.22.4ubuntu5_all.deb ...
174s Unpacking libdpkg-perl (1.22.4ubuntu5) ...
174s Selecting previously unselected package make.
174s Preparing to unpack .../5-make_4.3-4.1build1_arm64.deb ...
174s Unpacking make (4.3-4.1build1) ...
174s Selecting previously unselected package lto-disabled-list.
174s Preparing to unpack .../6-lto-disabled-list_47_all.deb ...
174s Unpacking lto-disabled-list (47) ...
174s Selecting previously unselected package dpkg-dev.
174s Preparing to unpack .../7-dpkg-dev_1.22.4ubuntu5_all.deb ...
175s Unpacking dpkg-dev (1.22.4ubuntu5) ...
175s Setting up lto-disabled-list (47) ...
175s Setting up libgdbm-compat4t64:arm64 (1.23-5.1) ...
175s Setting up make (4.3-4.1build1) ...
175s Setting up perl-modules-5.38 (5.38.2-3.2) ...
175s Setting up libperl5.38t64:arm64 (5.38.2-3.2) ...
175s Setting up perl (5.38.2-3.2) ...
175s Setting up libdpkg-perl (1.22.4ubuntu5) ...
175s Setting up dpkg-dev (1.22.4ubuntu5) ...
175s Processing triggers for man-db (2.12.0-3) ...
176s Processing triggers for libc-bin (2.39-0ubuntu2) ...
176s Reading package lists...
176s Building dependency tree...
176s Reading state information...
177s The following packages will be REMOVED:
177s   cloud-init* python3-configobj* python3-debconf*
178s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
178s After this operation, 3248 kB disk space will be freed.
178s (Reading database ... 
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(Reading database ... 74750 files and directories currently installed.)
178s Removing cloud-init (24.1-0ubuntu1) ...
179s Removing python3-configobj (5.0.8-3) ...
179s Removing python3-debconf (1.5.86) ...
179s Processing triggers for man-db (2.12.0-3) ...
180s (Reading database ... 
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(Reading database ... 74361 files and directories currently installed.)
180s Purging configuration files for cloud-init (24.1-0ubuntu1) ...
180s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
180s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
181s Reading package lists...
181s Building dependency tree...
181s Reading state information...
182s linux-generic is already the newest version (6.8.0-11.11+1).
182s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
182s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
182s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
183s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
183s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
184s Reading package lists...
184s Reading package lists...
184s Building dependency tree...
184s Reading state information...
185s Calculating upgrade...
185s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
185s Reading package lists...
186s Building dependency tree...
186s Reading state information...
186s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
187s autopkgtest [03:51:18]: rebooting testbed after setup commands that affected boot
218s autopkgtest [03:51:49]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
218s autopkgtest [03:51:49]: testbed dpkg architecture: arm64
219s autopkgtest [03:51:50]: @@@@@@@@@@@@@@@@@@@@ apt-source rsem
223s Get:1 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (dsc) [2249 B]
223s Get:2 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (tar) [275 kB]
223s Get:3 http://ftpmaster.internal/ubuntu noble/universe rsem 1.3.3+dfsg-3 (diff) [35.7 MB]
224s gpgv: Signature made Mon Dec 18 13:04:45 2023 UTC
224s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
224s gpgv:                issuer "emollier@debian.org"
224s gpgv: Can't check signature: No public key
224s dpkg-source: warning: cannot verify inline signature for ./rsem_1.3.3+dfsg-3.dsc: no acceptable signature found
224s autopkgtest [03:51:55]: testing package rsem version 1.3.3+dfsg-3
224s autopkgtest [03:51:55]: build not needed
226s autopkgtest [03:51:57]: test run-unit-test: preparing testbed
228s Reading package lists...
229s Building dependency tree...
229s Reading state information...
229s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
229s Starting 2 pkgProblemResolver with broken count: 0
229s Done
229s  Done
230s Starting pkgProblemResolver with broken count: 0
230s Starting 2 pkgProblemResolver with broken count: 0
230s Done
230s The following additional packages will be installed:
230s   bowtie fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
230s   libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5
230s   libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0
230s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
230s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
230s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
230s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
230s   r-base-core rsem unzip x11-common xdg-utils zip
230s Suggested packages:
230s   bowtie-examples tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib
230s   r-base-html r-bioc-ebseq hisat2
230s Recommended packages:
230s   r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl
230s   libx11-protocol-perl x11-utils x11-xserver-utils
230s The following NEW packages will be installed:
230s   bowtie fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
230s   libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5
230s   libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libjbig0
230s   libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0
230s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
230s   libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6
230s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
230s   r-base-core rsem unzip x11-common xdg-utils zip
231s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
231s 1 not fully installed or removed.
231s Need to get 74.5 MB of archives.
231s After this operation, 120 MB of additional disk space will be used.
231s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
231s Get:2 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB]
231s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB]
231s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB]
231s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB]
231s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB]
231s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B]
231s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
231s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
231s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
231s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
231s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
231s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
231s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
231s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
231s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
231s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
231s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
231s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
231s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
231s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
231s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
231s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
231s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
231s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
231s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
231s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
231s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
231s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
231s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
231s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
231s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
231s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
231s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
231s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
231s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
231s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
231s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
231s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
231s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
232s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
232s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
232s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB]
232s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB]
232s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB]
232s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB]
232s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 bowtie arm64 1.3.1-3 [1346 kB]
232s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 rsem arm64 1.3.3+dfsg-3 [36.0 MB]
234s Preconfiguring packages ...
234s Fetched 74.5 MB in 3s (26.9 MB/s)
234s Selecting previously unselected package libdeflate0:arm64.
234s (Reading database ... 
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(Reading database ... 74306 files and directories currently installed.)
234s Preparing to unpack .../00-libdeflate0_1.19-1_arm64.deb ...
234s Unpacking libdeflate0:arm64 (1.19-1) ...
234s Selecting previously unselected package libhtscodecs2:arm64.
234s Preparing to unpack .../01-libhtscodecs2_1.6.0-1_arm64.deb ...
234s Unpacking libhtscodecs2:arm64 (1.6.0-1) ...
234s Selecting previously unselected package libhts3:arm64.
234s Preparing to unpack .../02-libhts3_1.18+ds-1_arm64.deb ...
234s Unpacking libhts3:arm64 (1.18+ds-1) ...
234s Selecting previously unselected package zip.
234s Preparing to unpack .../03-zip_3.0-13_arm64.deb ...
234s Unpacking zip (3.0-13) ...
234s Selecting previously unselected package unzip.
234s Preparing to unpack .../04-unzip_6.0-28ubuntu3_arm64.deb ...
234s Unpacking unzip (6.0-28ubuntu3) ...
234s Selecting previously unselected package libpaper1:arm64.
234s Preparing to unpack .../05-libpaper1_1.1.29_arm64.deb ...
234s Unpacking libpaper1:arm64 (1.1.29) ...
234s Selecting previously unselected package libpaper-utils.
234s Preparing to unpack .../06-libpaper-utils_1.1.29_arm64.deb ...
234s Unpacking libpaper-utils (1.1.29) ...
234s Selecting previously unselected package xdg-utils.
234s Preparing to unpack .../07-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
234s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
234s Selecting previously unselected package libblas3:arm64.
234s Preparing to unpack .../08-libblas3_3.12.0-3_arm64.deb ...
234s Unpacking libblas3:arm64 (3.12.0-3) ...
234s Selecting previously unselected package fonts-dejavu-mono.
234s Preparing to unpack .../09-fonts-dejavu-mono_2.37-8_all.deb ...
234s Unpacking fonts-dejavu-mono (2.37-8) ...
234s Selecting previously unselected package fonts-dejavu-core.
234s Preparing to unpack .../10-fonts-dejavu-core_2.37-8_all.deb ...
234s Unpacking fonts-dejavu-core (2.37-8) ...
234s Selecting previously unselected package fontconfig-config.
234s Preparing to unpack .../11-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
235s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
235s Selecting previously unselected package libfontconfig1:arm64.
235s Preparing to unpack .../12-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
235s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
235s Selecting previously unselected package libpixman-1-0:arm64.
235s Preparing to unpack .../13-libpixman-1-0_0.42.2-1_arm64.deb ...
235s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
235s Selecting previously unselected package libxcb-render0:arm64.
235s Preparing to unpack .../14-libxcb-render0_1.15-1_arm64.deb ...
235s Unpacking libxcb-render0:arm64 (1.15-1) ...
235s Selecting previously unselected package libxcb-shm0:arm64.
235s Preparing to unpack .../15-libxcb-shm0_1.15-1_arm64.deb ...
235s Unpacking libxcb-shm0:arm64 (1.15-1) ...
235s Selecting previously unselected package libxrender1:arm64.
235s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
235s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
235s Selecting previously unselected package libcairo2:arm64.
235s Preparing to unpack .../17-libcairo2_1.18.0-1_arm64.deb ...
235s Unpacking libcairo2:arm64 (1.18.0-1) ...
235s Selecting previously unselected package libgomp1:arm64.
235s Preparing to unpack .../18-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
235s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
235s Selecting previously unselected package libjpeg-turbo8:arm64.
235s Preparing to unpack .../19-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
235s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
235s Selecting previously unselected package libjpeg8:arm64.
235s Preparing to unpack .../20-libjpeg8_8c-2ubuntu11_arm64.deb ...
235s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
235s Selecting previously unselected package libgfortran5:arm64.
235s Preparing to unpack .../21-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
235s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
235s Selecting previously unselected package liblapack3:arm64.
235s Preparing to unpack .../22-liblapack3_3.12.0-3_arm64.deb ...
235s Unpacking liblapack3:arm64 (3.12.0-3) ...
235s Selecting previously unselected package fontconfig.
235s Preparing to unpack .../23-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
235s Unpacking fontconfig (2.15.0-1ubuntu1) ...
235s Selecting previously unselected package libgraphite2-3:arm64.
236s Preparing to unpack .../24-libgraphite2-3_1.3.14-2_arm64.deb ...
236s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
236s Selecting previously unselected package libharfbuzz0b:arm64.
236s Preparing to unpack .../25-libharfbuzz0b_8.3.0-2_arm64.deb ...
236s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
236s Selecting previously unselected package libthai-data.
236s Preparing to unpack .../26-libthai-data_0.1.29-2_all.deb ...
236s Unpacking libthai-data (0.1.29-2) ...
236s Selecting previously unselected package libdatrie1:arm64.
236s Preparing to unpack .../27-libdatrie1_0.2.13-3_arm64.deb ...
236s Unpacking libdatrie1:arm64 (0.2.13-3) ...
236s Selecting previously unselected package libthai0:arm64.
236s Preparing to unpack .../28-libthai0_0.1.29-2_arm64.deb ...
236s Unpacking libthai0:arm64 (0.1.29-2) ...
236s Selecting previously unselected package libpango-1.0-0:arm64.
236s Preparing to unpack .../29-libpango-1.0-0_1.51.0+ds-4_arm64.deb ...
236s Unpacking libpango-1.0-0:arm64 (1.51.0+ds-4) ...
236s Selecting previously unselected package libpangoft2-1.0-0:arm64.
236s Preparing to unpack .../30-libpangoft2-1.0-0_1.51.0+ds-4_arm64.deb ...
236s Unpacking libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
236s Selecting previously unselected package libpangocairo-1.0-0:arm64.
236s Preparing to unpack .../31-libpangocairo-1.0-0_1.51.0+ds-4_arm64.deb ...
236s Unpacking libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
236s Selecting previously unselected package libtcl8.6:arm64.
236s Preparing to unpack .../32-libtcl8.6_8.6.13+dfsg-2_arm64.deb ...
236s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ...
236s Selecting previously unselected package libjbig0:arm64.
236s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
236s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
236s Selecting previously unselected package liblerc4:arm64.
236s Preparing to unpack .../34-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
236s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
236s Selecting previously unselected package libsharpyuv0:arm64.
236s Preparing to unpack .../35-libsharpyuv0_1.3.2-0.4_arm64.deb ...
236s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
236s Selecting previously unselected package libwebp7:arm64.
236s Preparing to unpack .../36-libwebp7_1.3.2-0.4_arm64.deb ...
236s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
236s Selecting previously unselected package libtiff6:arm64.
236s Preparing to unpack .../37-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
236s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
236s Selecting previously unselected package libxft2:arm64.
236s Preparing to unpack .../38-libxft2_2.3.6-1_arm64.deb ...
236s Unpacking libxft2:arm64 (2.3.6-1) ...
236s Selecting previously unselected package x11-common.
236s Preparing to unpack .../39-x11-common_1%3a7.7+23ubuntu2_all.deb ...
236s Unpacking x11-common (1:7.7+23ubuntu2) ...
236s Selecting previously unselected package libxss1:arm64.
237s Preparing to unpack .../40-libxss1_1%3a1.2.3-1build2_arm64.deb ...
237s Unpacking libxss1:arm64 (1:1.2.3-1build2) ...
237s Selecting previously unselected package libtk8.6:arm64.
237s Preparing to unpack .../41-libtk8.6_8.6.13-2_arm64.deb ...
237s Unpacking libtk8.6:arm64 (8.6.13-2) ...
237s Selecting previously unselected package libice6:arm64.
237s Preparing to unpack .../42-libice6_2%3a1.0.10-1build2_arm64.deb ...
237s Unpacking libice6:arm64 (2:1.0.10-1build2) ...
237s Selecting previously unselected package libsm6:arm64.
237s Preparing to unpack .../43-libsm6_2%3a1.2.3-1build2_arm64.deb ...
237s Unpacking libsm6:arm64 (2:1.2.3-1build2) ...
237s Selecting previously unselected package libxt6:arm64.
237s Preparing to unpack .../44-libxt6_1%3a1.2.1-1.1_arm64.deb ...
237s Unpacking libxt6:arm64 (1:1.2.1-1.1) ...
237s Selecting previously unselected package r-base-core.
237s Preparing to unpack .../45-r-base-core_4.3.2-1build1_arm64.deb ...
237s Unpacking r-base-core (4.3.2-1build1) ...
237s Selecting previously unselected package bowtie.
237s Preparing to unpack .../46-bowtie_1.3.1-3_arm64.deb ...
237s Unpacking bowtie (1.3.1-3) ...
237s Selecting previously unselected package rsem.
237s Preparing to unpack .../47-rsem_1.3.3+dfsg-3_arm64.deb ...
237s Unpacking rsem (1.3.3+dfsg-3) ...
237s Setting up libhtscodecs2:arm64 (1.6.0-1) ...
237s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
237s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
237s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
237s Setting up libpaper1:arm64 (1.1.29) ...
238s 
238s Creating config file /etc/papersize with new version
238s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
238s Setting up bowtie (1.3.1-3) ...
238s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
238s Setting up libdatrie1:arm64 (0.2.13-3) ...
238s Setting up libxcb-render0:arm64 (1.15-1) ...
238s Setting up unzip (6.0-28ubuntu3) ...
238s Setting up x11-common (1:7.7+23ubuntu2) ...
238s Setting up libdeflate0:arm64 (1.19-1) ...
238s Setting up libxcb-shm0:arm64 (1.15-1) ...
238s Setting up libpaper-utils (1.1.29) ...
238s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
238s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
238s Setting up zip (3.0-13) ...
238s Setting up libblas3:arm64 (3.12.0-3) ...
238s 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
238s Setting up fonts-dejavu-mono (2.37-8) ...
238s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ...
238s Setting up fonts-dejavu-core (2.37-8) ...
238s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
238s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
238s Setting up libwebp7:arm64 (1.3.2-0.4) ...
238s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
238s Setting up libthai-data (0.1.29-2) ...
238s Setting up libxss1:arm64 (1:1.2.3-1build2) ...
238s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
238s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
238s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
238s Setting up libice6:arm64 (2:1.0.10-1build2) ...
238s Setting up liblapack3:arm64 (3.12.0-3) ...
238s 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
238s Setting up libhts3:arm64 (1.18+ds-1) ...
238s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
239s Setting up libthai0:arm64 (0.1.29-2) ...
239s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
239s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
239s Setting up libsm6:arm64 (2:1.2.3-1build2) ...
239s Setting up fontconfig (2.15.0-1ubuntu1) ...
241s Regenerating fonts cache... done.
241s Setting up libxft2:arm64 (2.3.6-1) ...
241s Setting up libtk8.6:arm64 (8.6.13-2) ...
241s Setting up libpango-1.0-0:arm64 (1.51.0+ds-4) ...
241s Setting up libcairo2:arm64 (1.18.0-1) ...
241s Setting up libxt6:arm64 (1:1.2.1-1.1) ...
241s Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-4) ...
241s Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-4) ...
241s Setting up r-base-core (4.3.2-1build1) ...
241s 
241s Creating config file /etc/R/Renviron with new version
241s Setting up rsem (1.3.3+dfsg-3) ...
241s Setting up autopkgtest-satdep (0) ...
241s Processing triggers for man-db (2.12.0-3) ...
242s Processing triggers for install-info (7.1-3) ...
242s Processing triggers for libc-bin (2.39-0ubuntu2) ...
248s (Reading database ... 76410 files and directories currently installed.)
248s Removing autopkgtest-satdep (0) ...
249s autopkgtest [03:52:20]: test run-unit-test: [-----------------------
249s + pkg=rsem
249s + '[' /tmp/autopkgtest.kOBRUC/autopkgtest_tmp = '' ']'
249s + cp -a /usr/share/doc/rsem/examples/mouse_ref_building_from_transcripts.tar.gz /tmp/autopkgtest.kOBRUC/autopkgtest_tmp
249s + cd /tmp/autopkgtest.kOBRUC/autopkgtest_tmp
249s + tar -C . -xzf mouse_ref_building_from_transcripts.tar.gz
250s + rsem-prepare-reference --transcript-to-gene-map mouse_ref_mapping.txt mouse_ref.fa mouse_ref
250s rsem-synthesis-reference-transcripts mouse_ref 0 1 mouse_ref_mapping.txt mouse_ref.fa
255s Transcript Information File is generated!
255s Group File is generated!
255s Extracted Sequences File is generated!
255s 
255s rsem-preref mouse_ref.transcripts.fa 1 mouse_ref
258s Refs.makeRefs finished!
258s Refs.saveRefs finished!
258s mouse_ref.idx.fa is generated!
258s mouse_ref.n2g.idx.fa is generated!
258s 
258s autopkgtest [03:52:29]: test run-unit-test: -----------------------]
259s autopkgtest [03:52:30]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
259s run-unit-test        PASS
259s autopkgtest [03:52:30]: @@@@@@@@@@@@@@@@@@@@ summary
259s run-unit-test        PASS
271s Creating nova instance adt-noble-arm64-rsem-20240311-034810-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240311.img (UUID 900cfff9-7f1a-42c7-81a7-22635cd2a5f9)...