0s autopkgtest [15:23:51]: starting date and time: 2025-03-15 15:23:51+0000 0s autopkgtest [15:23:51]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:23:51]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v3fjhmq3/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 profphd-utils --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.9 lxd-armhf-10.145.243.9:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [15:24:12]: testbed dpkg architecture: armhf 23s autopkgtest [15:24:14]: testbed apt version: 2.9.33 27s autopkgtest [15:24:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [15:24:20]: testbed release detected to be: None 38s autopkgtest [15:24:29]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 40s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 40s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 40s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 41s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 41s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 43s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 43s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 43s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 43s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 45s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 48s Fetched 41.0 MB in 8s (5079 kB/s) 49s Reading package lists... 56s autopkgtest [15:24:47]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 59s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 60s Starting 2 pkgProblemResolver with broken count: 0 60s Done 61s Entering ResolveByKeep 62s 62s Calculating upgrade... 63s The following packages will be upgraded: 63s libc-bin libc6 locales python3-jinja2 sos strace 63s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 8642 kB of archives. 63s After this operation, 23.6 kB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 65s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 66s Preconfiguring packages ... 67s Fetched 8642 kB in 2s (3598 kB/s) 67s (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.) 67s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 67s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 67s Setting up libc6:armhf (2.41-1ubuntu2) ... 67s (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.) 67s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 67s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 68s Setting up libc-bin (2.41-1ubuntu2) ... 68s (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.) 68s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 68s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 68s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 68s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 68s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 68s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 68s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 69s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 69s Setting up sos (4.9.0-5) ... 70s Setting up locales (2.41-1ubuntu2) ... 71s Generating locales (this might take a while)... 73s en_US.UTF-8... done 73s Generation complete. 73s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 73s Setting up strace (6.13+ds-1ubuntu1) ... 73s Processing triggers for man-db (2.13.0-1) ... 75s Processing triggers for systemd (257.3-1ubuntu3) ... 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s Starting pkgProblemResolver with broken count: 0 79s Starting 2 pkgProblemResolver with broken count: 0 79s Done 80s Solving dependencies... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [15:25:14]: rebooting testbed after setup commands that affected boot 124s autopkgtest [15:25:55]: 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 149s autopkgtest [15:26:20]: @@@@@@@@@@@@@@@@@@@@ apt-source profphd-utils 160s Get:1 http://ftpmaster.internal/ubuntu plucky/universe profphd-utils 1.0.10-7 (dsc) [2056 B] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/universe profphd-utils 1.0.10-7 (tar) [388 kB] 160s Get:3 http://ftpmaster.internal/ubuntu plucky/universe profphd-utils 1.0.10-7 (diff) [7928 B] 160s gpgv: Signature made Fri Jan 21 14:22:49 2022 UTC 160s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 160s gpgv: issuer "tille@debian.org" 160s gpgv: Can't check signature: No public key 160s dpkg-source: warning: cannot verify inline signature for ./profphd-utils_1.0.10-7.dsc: no acceptable signature found 160s autopkgtest [15:26:31]: testing package profphd-utils version 1.0.10-7 162s autopkgtest [15:26:33]: build not needed 165s autopkgtest [15:26:36]: test convert-seq-test: preparing testbed 167s Reading package lists... 167s Building dependency tree... 167s Reading state information... 168s Starting pkgProblemResolver with broken count: 0 169s Starting 2 pkgProblemResolver with broken count: 0 169s Done 171s The following NEW packages will be installed: 171s libgfortran5 profphd-utils 171s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 171s Need to get 597 kB of archives. 171s After this operation, 1697 kB of additional disk space will be used. 171s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 171s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf profphd-utils armhf 1.0.10-7 [267 kB] 172s Fetched 597 kB in 1s (761 kB/s) 172s Selecting previously unselected package libgfortran5:armhf. 172s (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.) 172s Preparing to unpack .../libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 172s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 172s Selecting previously unselected package profphd-utils. 172s Preparing to unpack .../profphd-utils_1.0.10-7_armhf.deb ... 172s Unpacking profphd-utils (1.0.10-7) ... 173s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 173s Setting up profphd-utils (1.0.10-7) ... 173s Processing triggers for libc-bin (2.41-1ubuntu2) ... 173s Processing triggers for man-db (2.13.0-1) ... 187s autopkgtest [15:26:58]: test convert-seq-test: [----------------------- 190s =============================================================================== 190s Name of input sequence file : 190s 190s Enter string of length < *** [CR=default] 190s 190s Default: 190s 190s echo: 1ppt.hssp 190s --- number of alignments: 15 190s --- PROTEINS block done 190s ALIGNMENTS block done 190s PROFILE block done 190s ReadHSSP: 1ppt.hssp OK 190s =============================================================================== 190s Output-format? [*m*]: m = MSF 190s h = HSSP 190s p = PIR 190s f = FASTA/Pearson 190s d = DAF 190s y = PHYLIP 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: m 190s 190s echo: m 190s =============================================================================== 190s Do you want to select a fragment of this alignment?[*N*] 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: N 190s 190s echo: N 190s =============================================================================== 190s output file name ? 190s 190s Enter string of length < *** [CR=default] 190s 190s Default: 1ppt.msf 190s 190s echo: 1ppt.msf 190s =============================================================================== 190s Expand sequences according to HSSP insertion list ? 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: N 190s 190s echo: N 190s =============================================================================== 190s write another format ? 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: N 190s 190s echo: N 190s =============================================================================== 190s Name of input sequence file : 190s 190s Enter string of length < *** [CR=default] 190s 190s Default: 190s 190s echo: 1ppt.hssp 190s --- number of alignments: 15 190s --- PROTEINS block done 190s ALIGNMENTS block done 190s PROFILE block done 190s ReadHSSP: 1ppt.hssp OK 190s =============================================================================== 190s Output-format? [*m*]: m = MSF 190s h = HSSP 190s p = PIR 190s f = FASTA/Pearson 190s d = DAF 190s y = PHYLIP 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: m 190s 190s echo: y 190s =============================================================================== 190s Do you want to select a fragment of this alignment?[*N*] 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: N 190s 190s echo: N 190s =============================================================================== 190s output file name ? 190s 190s Enter string of length < *** [CR=default] 190s 190s Default: 1ppt.phy 190s 190s echo: 1ppt.phy 190s =============================================================================== 190s write another format ? 190s 190s Enter string of length < 1 [CR=default] 190s 190s Default: N 190s 190s echo: N 190s autopkgtest [15:27:01]: test convert-seq-test: -----------------------] 195s convert-seq-test PASS 195s autopkgtest [15:27:06]: test convert-seq-test: - - - - - - - - - - results - - - - - - - - - - 199s autopkgtest [15:27:10]: test filter-hssp-test: preparing testbed 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 204s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 212s autopkgtest [15:27:23]: test filter-hssp-test: [----------------------- 214s 214s **************************** HSSP-FILE FILTER ******************************** 214s R. Schneider, 1990 and later, EMBL-Heidelberg 214s ****************************************************************************** 214s 214s If you want to exclude an alignment independent from the threshold, mark the 214s alignment in your "personal" copy of the HSSP-file in the following way: 214s 214s type a character (non blank, overstrike mode) after the alignment number 214s in the PROTEINS-block, like the "*" in: 214s 214s 15*: REV1_YEAST 214s ^ 214s =============================================================================== 214s HSSP input file ? 214s 214s Enter string of length < 132 [CR=default] 214s 214s Default: 214s 214s echo: 1ppt.hssp 214s =============================================================================== 214s HSSP output file ? 214s 214s Enter string of length < 132 [CR=default] 214s 214s Default: 214s echo: 1ppt_filtered.hssp 214s =============================================================================== 214s metric file (HSSP-VARIABILITY) ? 214s 214s Enter string of length < 132 [CR=default] 214s 214s Default: /home/rost/pub/max/mat/Maxhom_GCG.metric 214s 214s echo: Maxhom_GCG.metric 214s =============================================================================== 214s BR 1999 threshold ? 214s 214s formula+x : formula value plus x percent 214s ALL : no threshold or 214s "file name" : with threshold specification 214s 214s Enter string of length < 80 [CR=default] 214s 214s Default: formula+5 214s 214s echo: formula+5 214s =============================================================================== 214s exclude too similar pairs? 214s positive real number < 1 (like: 0.8) 214s 214s Enter string of length < 80 [CR=default] 214s 214s Default: 1.00 214s 214s echo: 1.00 214s =============================================================================== 214s clean up 100% identical pairs ? 214s 214s Enter string of length < 80 [CR=default] 214s 214s Default: NO 214s 214s echo: NO 214s =============================================================================== 214s write distance table ? 214s NO : default no file written 214s YES : default file = PDBid_distance.table 214s FILE_NAME : written into this file written 214s 214s 214s Enter string of length < 132 [CR=default] 214s 214s Default: NO 214s 214s echo: NO 214s use formula value + 5 % 214s ============================================================================== 214s --- number of alignments: 15 214s --- PROTEINS block done 214s ALIGNMENTS block done 214s PROFILE block done 214s ReadHSSP: 1ppt.hssp OK 214s GETSIMMATRIX open metric: Maxhom_GCG.metric 214s STRUCTURE-STATES_1: 1 214s I/O-STATES_1 : 1 214s STRUCTURE-STATES_2: 1 214s I/O-STATES_2 : 1 214s ============================================================================== 214s 1. ALIGNMENT excluded: threshold 214s 2. ALIGNMENT excluded: threshold 214s 3. ALIGNMENT excluded: threshold 214s 6. ALIGNMENT excluded: threshold 214s 7. ALIGNMENT excluded: threshold 214s 8. ALIGNMENT excluded: threshold 214s 9. ALIGNMENT excluded: threshold 214s 10. ALIGNMENT excluded: threshold 214s 11. ALIGNMENT excluded: threshold 214s 12. ALIGNMENT excluded: threshold 214s 13. ALIGNMENT excluded: threshold 214s 14. ALIGNMENT excluded: threshold 214s 15. ALIGNMENT excluded: threshold 214s SETCONSERVATION: sum over matrix: -1.93333626E-03 214s smin is : -0.915574968 214s --- GETCONSWEIGHT_BR begin 214s GETCONSWEIGHT: SUM,MEAN 26.4319096 0.734219730 214s --- GETCONSWEIGHT_BR ended 214s calc_var 214s CALC_PROF 215s autopkgtest [15:27:26]: test filter-hssp-test: -----------------------] 219s autopkgtest [15:27:30]: test filter-hssp-test: - - - - - - - - - - results - - - - - - - - - - 219s filter-hssp-test PASS 222s autopkgtest [15:27:33]: @@@@@@@@@@@@@@@@@@@@ summary 222s convert-seq-test PASS 222s filter-hssp-test PASS