0s autopkgtest [15:14:25]: starting date and time: 2025-03-15 15:14:25+0000 0s autopkgtest [15:14:25]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:14:25]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.owprsp_i/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade phast --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.197 lxd-armhf-10.145.243.197:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [15:14:46]: testbed dpkg architecture: armhf 23s autopkgtest [15:14:48]: testbed apt version: 2.9.33 26s autopkgtest [15:14:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [15:14:53]: testbed release detected to be: None 36s autopkgtest [15:15:01]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 41s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 42s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 59s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 60s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 60s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 60s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 75s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 77s Fetched 41.0 MB in 38s (1071 kB/s) 78s Reading package lists... 84s autopkgtest [15:15:49]: upgrading testbed (apt dist-upgrade and autopurge) 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 88s Entering ResolveByKeep 88s 88s Calculating upgrade... 89s The following packages will be upgraded: 89s libc-bin libc6 locales python3-jinja2 sos strace 89s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 8642 kB of archives. 89s After this operation, 23.6 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 91s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 95s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 96s Preconfiguring packages ... 97s Fetched 8642 kB in 7s (1194 kB/s) 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 97s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 97s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 97s Setting up libc6:armhf (2.41-1ubuntu2) ... 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 97s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 97s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 97s Setting up libc-bin (2.41-1ubuntu2) ... 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 98s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 98s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 98s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 98s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 98s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 98s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 98s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 99s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 99s Setting up sos (4.9.0-5) ... 99s Setting up locales (2.41-1ubuntu2) ... 100s Generating locales (this might take a while)... 102s en_US.UTF-8... done 102s Generation complete. 102s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 103s Setting up strace (6.13+ds-1ubuntu1) ... 103s Processing triggers for man-db (2.13.0-1) ... 104s Processing triggers for systemd (257.3-1ubuntu3) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 108s Solving dependencies... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [15:16:15]: rebooting testbed after setup commands that affected boot 152s autopkgtest [15:16:57]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 186s autopkgtest [15:17:31]: @@@@@@@@@@@@@@@@@@@@ apt-source phast 199s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phast 1.7+dfsg-2 (dsc) [2218 B] 199s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phast 1.7+dfsg-2 (tar) [1810 kB] 199s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phast 1.7+dfsg-2 (diff) [58.7 kB] 199s gpgv: Signature made Sun Jan 5 20:19:26 2025 UTC 199s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 199s gpgv: issuer "emollier@debian.org" 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./phast_1.7+dfsg-2.dsc: no acceptable signature found 199s autopkgtest [15:17:44]: testing package phast version 1.7+dfsg-2 201s autopkgtest [15:17:46]: build not needed 204s autopkgtest [15:17:49]: test run-unit-test: preparing testbed 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 208s The following NEW packages will be installed: 208s libblas3 libgfortran5 liblapack3 phast 208s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 5541 kB of archives. 208s After this operation, 26.7 MB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 210s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf phast armhf 1.7+dfsg-2 [2988 kB] 212s Fetched 5541 kB in 4s (1290 kB/s) 212s Selecting previously unselected package libblas3:armhf. 212s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 212s Preparing to unpack .../libblas3_3.12.1-2_armhf.deb ... 212s Unpacking libblas3:armhf (3.12.1-2) ... 213s Selecting previously unselected package libgfortran5:armhf. 213s Preparing to unpack .../libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 213s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 213s Selecting previously unselected package liblapack3:armhf. 213s Preparing to unpack .../liblapack3_3.12.1-2_armhf.deb ... 213s Unpacking liblapack3:armhf (3.12.1-2) ... 213s Selecting previously unselected package phast. 213s Preparing to unpack .../phast_1.7+dfsg-2_armhf.deb ... 213s Unpacking phast (1.7+dfsg-2) ... 213s Setting up libblas3:armhf (3.12.1-2) ... 213s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 213s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 213s Setting up liblapack3:armhf (3.12.1-2) ... 213s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 213s Setting up phast (1.7+dfsg-2) ... 213s Processing triggers for man-db (2.13.0-1) ... 213s Processing triggers for libc-bin (2.41-1ubuntu2) ... 222s autopkgtest [15:18:07]: test run-unit-test: [----------------------- 224s *** Testing msa_view *** 224s msa_view hmrc.ss -i SS --end 10000 > hmrc.fa 224s if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.fa -o PHYLIP > hmrc.ph 224s msa_view hmrc.ph -i PHYLIP > hmrc.fa 224s if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm 224s msa_view hmrc.mpm --in-format MPM > hmrc.fa 224s if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.fa -o SS > hmrc_short_a.ss 224s msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss 224s if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi 224s msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa 224s msa_view --seqs human,cow hmrc.fa > hm_b.fa 224s if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa 224s msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa 224s if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa 224s msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa 224s if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa 224s msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa 224s if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi 224s msa_view hmrc.ss --summary -i SS > hmrc_summary 224s if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi 224s -e Passed all tests. 224s 225s autopkgtest [15:18:10]: test run-unit-test: -----------------------] 229s run-unit-test PASS 229s autopkgtest [15:18:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 233s autopkgtest [15:18:18]: @@@@@@@@@@@@@@@@@@@@ summary 233s run-unit-test PASS