0s autopkgtest [01:14:38]: starting date and time: 2024-06-08 01:14:38+0000 0s autopkgtest [01:14:38]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [01:14:38]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.su2g5v7i/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest --apt-upgrade python-pymbar --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-134.secgroup --name adt-oracular-i386-python-pymbar-20240608-011438-juju-7f2275-prod-proposed-migration-environment-3-afd6cc12-23f0-41c6-bbe6-b87bdb2c24a2 --image adt/ubuntu-oracular-amd64-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,keyserver.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/ 119s autopkgtest [01:16:37]: testbed dpkg architecture: amd64 120s autopkgtest [01:16:38]: testbed apt version: 2.9.3 120s autopkgtest [01:16:38]: test architecture: i386 120s autopkgtest [01:16:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 120s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 120s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 120s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 120s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 120s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 120s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [38.1 kB] 120s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [66.4 kB] 120s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 120s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 120s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [315 kB] 120s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [126 kB] 120s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [11.7 kB] 120s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 120s Fetched 1102 kB in 0s (4500 kB/s) 120s Reading package lists... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Calculating upgrade... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 124s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 124s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 125s Reading package lists... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s autopkgtest [01:16:45]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 127s autopkgtest [01:16:45]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 129s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (dsc) [2363 B] 129s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (tar) [17.1 MB] 129s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (diff) [3916 B] 129s gpgv: Signature made Wed Feb 1 21:01:41 2023 UTC 129s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 129s gpgv: issuer "emollier@debian.org" 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found 129s autopkgtest [01:16:47]: testing package python-pymbar version 3.1.0-4 130s autopkgtest [01:16:48]: build not needed 133s autopkgtest [01:16:51]: test command1: preparing testbed 137s Note, using file '/tmp/autopkgtest.aiNrIp/1-autopkgtest-satdep.dsc' to get the build dependencies 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 139s The following NEW packages will be installed: 139s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++ 139s g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base 139s gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libblas3 139s libcc1-0 libgcc-13-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 139s liblapack3 liblbfgsb0 liblsan0 libmpc3 libquadmath0 libstdc++-13-dev 139s libtsan2 libubsan1 python3-decorator python3-iniconfig python3-numpy 139s python3-packaging python3-pluggy python3-pymbar python3-pytest python3-scipy 139s 0 upgraded, 40 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 86.4 MB of archives. 139s After this operation, 322 MB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-base amd64 13.2.0-23ubuntu4 [49.0 kB] 139s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libisl23 amd64 0.26-3build1 [680 kB] 139s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB] 139s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [11.2 MB] 139s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13 amd64 13.2.0-23ubuntu4 [1032 B] 139s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 139s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 139s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libcc1-0 amd64 14.1.0-1ubuntu1 [48.0 kB] 139s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 139s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libitm1 amd64 14.1.0-1ubuntu1 [29.1 kB] 139s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libatomic1 amd64 14.1.0-1ubuntu1 [10.4 kB] 139s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libasan8 amd64 14.1.0-1ubuntu1 [3025 kB] 139s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 liblsan0 amd64 14.1.0-1ubuntu1 [1313 kB] 139s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libtsan2 amd64 14.1.0-1ubuntu1 [2736 kB] 139s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libubsan1 amd64 14.1.0-1ubuntu1 [1174 kB] 139s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libhwasan0 amd64 14.1.0-1ubuntu1 [1632 kB] 139s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libquadmath0 amd64 14.1.0-1ubuntu1 [153 kB] 139s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu4 [2688 kB] 139s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [21.9 MB] 139s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13 amd64 13.2.0-23ubuntu4 [482 kB] 139s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 139s Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 139s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu4 [2399 kB] 139s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [12.5 MB] 139s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13 amd64 13.2.0-23ubuntu4 [14.5 kB] 139s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 139s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 139s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 139s Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 139s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 139s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 139s Get:32 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 139s Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 139s Get:34 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 139s Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 139s Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 139s Get:37 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 139s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-10 [15.5 MB] 139s Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pymbar all 3.1.0-4 [67.8 kB] 139s Get:40 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 140s Fetched 86.4 MB in 1s (116 MB/s) 140s Selecting previously unselected package gcc-13-base:amd64. 140s (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 ... 74365 files and directories currently installed.) 140s Preparing to unpack .../00-gcc-13-base_13.2.0-23ubuntu4_amd64.deb ... 140s Unpacking gcc-13-base:amd64 (13.2.0-23ubuntu4) ... 140s Selecting previously unselected package libisl23:amd64. 140s Preparing to unpack .../01-libisl23_0.26-3build1_amd64.deb ... 140s Unpacking libisl23:amd64 (0.26-3build1) ... 140s Selecting previously unselected package libmpc3:amd64. 140s Preparing to unpack .../02-libmpc3_1.3.1-1build1_amd64.deb ... 140s Unpacking libmpc3:amd64 (1.3.1-1build1) ... 140s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 140s Preparing to unpack .../03-cpp-13-x86-64-linux-gnu_13.2.0-23ubuntu4_amd64.deb ... 140s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 140s Selecting previously unselected package cpp-13. 140s Preparing to unpack .../04-cpp-13_13.2.0-23ubuntu4_amd64.deb ... 140s Unpacking cpp-13 (13.2.0-23ubuntu4) ... 140s Selecting previously unselected package cpp-x86-64-linux-gnu. 140s Preparing to unpack .../05-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 140s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 140s Selecting previously unselected package cpp. 140s Preparing to unpack .../06-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 140s Unpacking cpp (4:13.2.0-7ubuntu1) ... 140s Selecting previously unselected package libcc1-0:amd64. 140s Preparing to unpack .../07-libcc1-0_14.1.0-1ubuntu1_amd64.deb ... 140s Unpacking libcc1-0:amd64 (14.1.0-1ubuntu1) ... 140s Selecting previously unselected package libgomp1:amd64. 140s Preparing to unpack .../08-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 140s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 140s Selecting previously unselected package libitm1:amd64. 140s Preparing to unpack .../09-libitm1_14.1.0-1ubuntu1_amd64.deb ... 140s Unpacking libitm1:amd64 (14.1.0-1ubuntu1) ... 140s Selecting previously unselected package libatomic1:amd64. 140s Preparing to unpack .../10-libatomic1_14.1.0-1ubuntu1_amd64.deb ... 140s Unpacking libatomic1:amd64 (14.1.0-1ubuntu1) ... 140s Selecting previously unselected package libasan8:amd64. 140s Preparing to unpack .../11-libasan8_14.1.0-1ubuntu1_amd64.deb ... 140s Unpacking libasan8:amd64 (14.1.0-1ubuntu1) ... 141s Selecting previously unselected package liblsan0:amd64. 141s Preparing to unpack .../12-liblsan0_14.1.0-1ubuntu1_amd64.deb ... 141s Unpacking liblsan0:amd64 (14.1.0-1ubuntu1) ... 141s Selecting previously unselected package libtsan2:amd64. 141s Preparing to unpack .../13-libtsan2_14.1.0-1ubuntu1_amd64.deb ... 141s Unpacking libtsan2:amd64 (14.1.0-1ubuntu1) ... 141s Selecting previously unselected package libubsan1:amd64. 141s Preparing to unpack .../14-libubsan1_14.1.0-1ubuntu1_amd64.deb ... 141s Unpacking libubsan1:amd64 (14.1.0-1ubuntu1) ... 141s Selecting previously unselected package libhwasan0:amd64. 141s Preparing to unpack .../15-libhwasan0_14.1.0-1ubuntu1_amd64.deb ... 141s Unpacking libhwasan0:amd64 (14.1.0-1ubuntu1) ... 141s Selecting previously unselected package libquadmath0:amd64. 141s Preparing to unpack .../16-libquadmath0_14.1.0-1ubuntu1_amd64.deb ... 141s Unpacking libquadmath0:amd64 (14.1.0-1ubuntu1) ... 141s Selecting previously unselected package libgcc-13-dev:amd64. 141s Preparing to unpack .../17-libgcc-13-dev_13.2.0-23ubuntu4_amd64.deb ... 141s Unpacking libgcc-13-dev:amd64 (13.2.0-23ubuntu4) ... 141s Selecting previously unselected package gcc-13-x86-64-linux-gnu. 141s Preparing to unpack .../18-gcc-13-x86-64-linux-gnu_13.2.0-23ubuntu4_amd64.deb ... 141s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 141s Selecting previously unselected package gcc-13. 141s Preparing to unpack .../19-gcc-13_13.2.0-23ubuntu4_amd64.deb ... 141s Unpacking gcc-13 (13.2.0-23ubuntu4) ... 141s Selecting previously unselected package gcc-x86-64-linux-gnu. 141s Preparing to unpack .../20-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 141s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 141s Selecting previously unselected package gcc. 141s Preparing to unpack .../21-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ... 141s Unpacking gcc (4:13.2.0-7ubuntu1) ... 141s Selecting previously unselected package libstdc++-13-dev:amd64. 141s Preparing to unpack .../22-libstdc++-13-dev_13.2.0-23ubuntu4_amd64.deb ... 141s Unpacking libstdc++-13-dev:amd64 (13.2.0-23ubuntu4) ... 142s Selecting previously unselected package g++-13-x86-64-linux-gnu. 142s Preparing to unpack .../23-g++-13-x86-64-linux-gnu_13.2.0-23ubuntu4_amd64.deb ... 142s Unpacking g++-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 142s Selecting previously unselected package g++-13. 142s Preparing to unpack .../24-g++-13_13.2.0-23ubuntu4_amd64.deb ... 142s Unpacking g++-13 (13.2.0-23ubuntu4) ... 142s Selecting previously unselected package g++-x86-64-linux-gnu. 142s Preparing to unpack .../25-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 142s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 142s Selecting previously unselected package g++. 142s Preparing to unpack .../26-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 142s Unpacking g++ (4:13.2.0-7ubuntu1) ... 142s Selecting previously unselected package build-essential. 142s Preparing to unpack .../27-build-essential_12.10ubuntu1_amd64.deb ... 142s Unpacking build-essential (12.10ubuntu1) ... 142s Selecting previously unselected package libblas3:amd64. 142s Preparing to unpack .../28-libblas3_3.12.0-3build1_amd64.deb ... 142s Unpacking libblas3:amd64 (3.12.0-3build1) ... 142s Selecting previously unselected package libgfortran5:amd64. 142s Preparing to unpack .../29-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 142s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 142s Selecting previously unselected package liblapack3:amd64. 142s Preparing to unpack .../30-liblapack3_3.12.0-3build1_amd64.deb ... 142s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 142s Selecting previously unselected package liblbfgsb0:amd64. 142s Preparing to unpack .../31-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 142s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 142s Selecting previously unselected package python3-decorator. 142s Preparing to unpack .../32-python3-decorator_5.1.1-5_all.deb ... 142s Unpacking python3-decorator (5.1.1-5) ... 142s Selecting previously unselected package python3-iniconfig. 142s Preparing to unpack .../33-python3-iniconfig_1.1.1-2_all.deb ... 142s Unpacking python3-iniconfig (1.1.1-2) ... 142s Selecting previously unselected package python3-numpy. 142s Preparing to unpack .../34-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 142s Unpacking python3-numpy (1:1.26.4+ds-10) ... 142s Selecting previously unselected package python3-packaging. 143s Preparing to unpack .../35-python3-packaging_24.0-1_all.deb ... 143s Unpacking python3-packaging (24.0-1) ... 143s Selecting previously unselected package python3-pluggy. 143s Preparing to unpack .../36-python3-pluggy_1.5.0-1_all.deb ... 143s Unpacking python3-pluggy (1.5.0-1) ... 143s Selecting previously unselected package python3-scipy. 143s Preparing to unpack .../37-python3-scipy_1.11.4-10_amd64.deb ... 143s Unpacking python3-scipy (1.11.4-10) ... 143s Selecting previously unselected package python3-pymbar. 143s Preparing to unpack .../38-python3-pymbar_3.1.0-4_all.deb ... 143s Unpacking python3-pymbar (3.1.0-4) ... 143s Selecting previously unselected package python3-pytest. 143s Preparing to unpack .../39-python3-pytest_8.2.2-1ubuntu1_all.deb ... 143s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 143s Setting up python3-iniconfig (1.1.1-2) ... 143s Setting up libgomp1:amd64 (14.1.0-1ubuntu1) ... 143s Setting up python3-decorator (5.1.1-5) ... 143s Setting up libblas3:amd64 (3.12.0-3build1) ... 143s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 143s Setting up python3-packaging (24.0-1) ... 144s Setting up gcc-13-base:amd64 (13.2.0-23ubuntu4) ... 144s Setting up libquadmath0:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libmpc3:amd64 (1.3.1-1build1) ... 144s Setting up libatomic1:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 144s Setting up python3-pluggy (1.5.0-1) ... 144s Setting up libubsan1:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libhwasan0:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libasan8:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libtsan2:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libisl23:amd64 (0.26-3build1) ... 144s Setting up libcc1-0:amd64 (14.1.0-1ubuntu1) ... 144s Setting up liblsan0:amd64 (14.1.0-1ubuntu1) ... 144s Setting up libitm1:amd64 (14.1.0-1ubuntu1) ... 144s Setting up liblapack3:amd64 (3.12.0-3build1) ... 144s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 144s Setting up cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 144s Setting up python3-pytest (8.2.2-1ubuntu1) ... 144s Setting up python3-numpy (1:1.26.4+ds-10) ... 146s Setting up libgcc-13-dev:amd64 (13.2.0-23ubuntu4) ... 146s Setting up libstdc++-13-dev:amd64 (13.2.0-23ubuntu4) ... 146s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 146s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 146s Setting up python3-scipy (1.11.4-10) ... 149s Setting up cpp-13 (13.2.0-23ubuntu4) ... 149s Setting up gcc-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 149s Setting up gcc-13 (13.2.0-23ubuntu4) ... 149s Setting up cpp (4:13.2.0-7ubuntu1) ... 149s Setting up python3-pymbar (3.1.0-4) ... 149s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 149s """A function that when zeroed is equivalent to the solution of 149s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 149s """ 149s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 149s """ 149s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 149s """ 149s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 149s """ 149s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 149s """ 149s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 149s """Compute estimate of overlap matrix between the states. 149s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 149s """Compute the free energy of occupying a number of bins. 149s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 149s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 149s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 149s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 149s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 149s """ 149s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 149s """Generate samples from forward and reverse Gaussian work distributions. 149s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 149s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 149s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 149s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 149s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 149s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 149s Setting up g++-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 149s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 149s Setting up gcc (4:13.2.0-7ubuntu1) ... 149s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 149s Setting up g++-13 (13.2.0-23ubuntu4) ... 149s Setting up g++ (4:13.2.0-7ubuntu1) ... 149s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 149s Setting up build-essential (12.10ubuntu1) ... 149s Processing triggers for man-db (2.12.1-1) ... 150s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 152s The following NEW packages will be installed: 152s autopkgtest-satdep 152s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 152s Need to get 0 B/696 B of archives. 152s After this operation, 0 B of additional disk space will be used. 152s Get:1 /tmp/autopkgtest.aiNrIp/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 152s Selecting previously unselected package autopkgtest-satdep. 152s (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 ... 78088 files and directories currently installed.) 152s Preparing to unpack .../2-autopkgtest-satdep.deb ... 152s Unpacking autopkgtest-satdep (0) ... 152s Setting up autopkgtest-satdep (0) ... 154s (Reading database ... 78088 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 159s autopkgtest [01:17:17]: test command1: rm pymbar/*.py && pytest-3 159s autopkgtest [01:17:17]: test command1: [----------------------- 160s ============================= test session starts ============================== 160s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 160s rootdir: /tmp/autopkgtest.aiNrIp/build.37J/src 160s collected 37 items 160s 160s pymbar/tests/test_bar.py .. [ 5%] 276s pymbar/tests/test_covariance.py ... [ 13%] 296s pymbar/tests/test_mbar.py ................ [ 56%] 321s pymbar/tests/test_mbar_solvers.py .... [ 67%] 325s pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] 326s pymbar/tests/test_utils.py ... [100%] 326s 326s =============================== warnings summary =============================== 326s ../../../../usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29 326s /usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 326s from pkg_resources import resource_filename 326s 326s pymbar/tests/test_bar.py: 4 warnings 326s pymbar/tests/test_covariance.py: 9 warnings 326s pymbar/tests/test_mbar.py: 8 warnings 326s pymbar/tests/test_mbar_solvers.py: 11 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:561: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s f_i = np.matrix(self.f_k) 326s 326s pymbar/tests/test_bar.py: 4 warnings 326s pymbar/tests/test_covariance.py: 3 warnings 326s pymbar/tests/test_mbar.py: 29 warnings 326s pymbar/tests/test_mbar_solvers.py: 11 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1772: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 326s 326s pymbar/tests/test_bar.py: 4 warnings 326s pymbar/tests/test_covariance.py: 3 warnings 326s pymbar/tests/test_mbar.py: 29 warnings 326s pymbar/tests/test_mbar_solvers.py: 11 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1773: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s W = np.matrix(W, dtype=np.float64) 326s 326s pymbar/tests/test_bar.py: 40 warnings 326s pymbar/tests/test_covariance.py: 78 warnings 326s pymbar/tests/test_mbar.py: 287 warnings 326s pymbar/tests/test_mbar_solvers.py: 99 warnings 326s /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s return matrix(data, dtype=dtype, copy=False) 326s 326s pymbar/tests/test_bar.py: 4 warnings 326s pymbar/tests/test_covariance.py: 3 warnings 326s pymbar/tests/test_mbar.py: 29 warnings 326s pymbar/tests/test_mbar_solvers.py: 11 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1783: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Sigma = np.matrix(np.diag(np.sqrt(S2))) 326s 326s pymbar/tests/test_bar.py: 4 warnings 326s pymbar/tests/test_covariance.py: 3 warnings 326s pymbar/tests/test_mbar.py: 29 warnings 326s pymbar/tests/test_mbar_solvers.py: 11 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1784: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s V = np.matrix(V) 326s 326s pymbar/tests/test_bar.py: 4 warnings 326s pymbar/tests/test_covariance.py: 9 warnings 326s pymbar/tests/test_mbar.py: 23 warnings 326s pymbar/tests/test_mbar_solvers.py: 11 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1636: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s diag = np.matrix(cov.diagonal()) 326s 326s pymbar/tests/test_bar.py::test_bar_computeOverlap 326s pymbar/tests/test_bar.py::test_bar_computeOverlap 326s /usr/lib/python3/dist-packages/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases 326s warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) 326s 326s pymbar/tests/test_bar.py::test_bar_computeOverlap 326s pymbar/tests/test_bar.py::test_bar_computeOverlap 326s pymbar/tests/test_bar.py::test_bar_computeOverlap 326s pymbar/tests/test_bar.py::test_bar_computeOverlap 326s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 326s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 326s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 326s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:485: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s W = np.matrix(self.getWeights(), np.float64) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1753: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1754: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s W = np.matrix(W, dtype=np.float64) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1759: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Sigma = np.matrix(np.diag(S)) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1760: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s V = np.matrix(Vt).T 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:385: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s f_i = np.matrix(self.f_k) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1925: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1926: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s W = np.matrix(W, dtype=np.float64) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1931: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Sigma = np.matrix(np.diag(S)) 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1932: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s V = np.matrix(Vt).T 326s 326s pymbar/tests/test_covariance.py::test_100x100_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_oscillators 326s pymbar/tests/test_covariance.py::test_200x50_exponentials 326s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1784: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) 326s 326s pymbar/tests/test_mbar.py: 560 warnings 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:579: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 326s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1088: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s A_im = np.matrix(inner_results['observables']) 326s 326s pymbar/tests/test_mbar.py: 16 warnings 326s /tmp/autopkgtest.aiNrIp/build.37J/src/pymbar/tests/test_mbar.py:23: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1377: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1382: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s f_k = np.matrix(inner_results['f']) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1389: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s u_k = np.matrix(inner_results['observables']) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s /tmp/autopkgtest.aiNrIp/build.37J/src/pymbar/tests/test_mbar.py:253: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s /tmp/autopkgtest.aiNrIp/build.37J/src/pymbar/tests/test_mbar.py:254: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 326s /tmp/autopkgtest.aiNrIp/build.37J/src/pymbar/tests/test_mbar.py:255: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 326s /tmp/autopkgtest.aiNrIp/build.37J/src/pymbar/tests/test_mbar.py:301: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) 326s 326s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 326s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 326s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 326s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 326s /usr/lib/python3/dist-packages/pymbar/mbar.py:1280: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 326s f_k = np.matrix(inner_results['f']) 326s 326s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 326s =========== 33 passed, 4 skipped, 1431 warnings in 166.41s (0:02:46) =========== 326s autopkgtest [01:20:04]: test command1: -----------------------] 326s autopkgtest [01:20:04]: test command1: - - - - - - - - - - results - - - - - - - - - - 326s command1 PASS 327s autopkgtest [01:20:05]: test autodep8-python3: preparing testbed 467s autopkgtest [01:22:25]: testbed dpkg architecture: amd64 467s autopkgtest [01:22:25]: testbed apt version: 2.9.3 467s autopkgtest [01:22:25]: test architecture: i386 467s autopkgtest [01:22:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 467s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 467s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 467s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 467s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 467s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 467s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [66.4 kB] 467s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [38.1 kB] 467s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 467s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 467s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [315 kB] 467s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [126 kB] 467s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 467s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [11.7 kB] 467s Fetched 1102 kB in 0s (4048 kB/s) 467s Reading package lists... 469s Reading package lists... 469s Building dependency tree... 469s Reading state information... 470s Calculating upgrade... 470s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 470s Reading package lists... 471s Building dependency tree... 471s Reading state information... 471s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 471s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 471s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 471s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 471s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 473s Reading package lists... 473s Reading package lists... 473s Building dependency tree... 473s Reading state information... 474s Calculating upgrade... 474s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 474s Reading package lists... 475s Building dependency tree... 475s Reading state information... 475s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 478s Note, using file '/tmp/autopkgtest.aiNrIp/3-autopkgtest-satdep.dsc' to get the build dependencies 478s Reading package lists... 478s Building dependency tree... 478s Reading state information... 479s Starting pkgProblemResolver with broken count: 0 479s Starting 2 pkgProblemResolver with broken count: 0 479s Done 479s The following NEW packages will be installed: 479s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++ 479s g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base 479s gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libatomic1 libblas3 479s libcc1-0 libgcc-13-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 479s liblapack3 liblbfgsb0 liblsan0 libmpc3 libquadmath0 libstdc++-13-dev 479s libtsan2 libubsan1 python3-all python3-decorator python3-numpy 479s python3-pymbar python3-scipy 479s 0 upgraded, 37 newly installed, 0 to remove and 0 not upgraded. 479s Need to get 86.1 MB of archives. 479s After this operation, 320 MB of additional disk space will be used. 479s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-base amd64 13.2.0-23ubuntu4 [49.0 kB] 479s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libisl23 amd64 0.26-3build1 [680 kB] 479s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB] 479s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [11.2 MB] 480s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13 amd64 13.2.0-23ubuntu4 [1032 B] 480s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 480s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 480s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libcc1-0 amd64 14.1.0-1ubuntu1 [48.0 kB] 480s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 480s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libitm1 amd64 14.1.0-1ubuntu1 [29.1 kB] 480s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libatomic1 amd64 14.1.0-1ubuntu1 [10.4 kB] 480s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libasan8 amd64 14.1.0-1ubuntu1 [3025 kB] 480s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 liblsan0 amd64 14.1.0-1ubuntu1 [1313 kB] 480s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libtsan2 amd64 14.1.0-1ubuntu1 [2736 kB] 480s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libubsan1 amd64 14.1.0-1ubuntu1 [1174 kB] 480s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libhwasan0 amd64 14.1.0-1ubuntu1 [1632 kB] 480s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libquadmath0 amd64 14.1.0-1ubuntu1 [153 kB] 480s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu4 [2688 kB] 480s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [21.9 MB] 480s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13 amd64 13.2.0-23ubuntu4 [482 kB] 480s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 480s Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 480s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu4 [2399 kB] 480s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [12.5 MB] 480s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13 amd64 13.2.0-23ubuntu4 [14.5 kB] 480s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 480s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 480s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 480s Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 480s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 480s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 480s Get:32 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 480s Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.3-0ubuntu1 [888 B] 480s Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 480s Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 480s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-10 [15.5 MB] 480s Get:37 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pymbar all 3.1.0-4 [67.8 kB] 481s Fetched 86.1 MB in 1s (127 MB/s) 481s Selecting previously unselected package gcc-13-base:amd64. 481s (Reading database ... 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(13.2.0-23ubuntu4) ... 484s Setting up libquadmath0:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libmpc3:amd64 (1.3.1-1build1) ... 484s Setting up libatomic1:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libubsan1:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libhwasan0:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libasan8:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libtsan2:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libisl23:amd64 (0.26-3build1) ... 484s Setting up libcc1-0:amd64 (14.1.0-1ubuntu1) ... 484s Setting up liblsan0:amd64 (14.1.0-1ubuntu1) ... 484s Setting up libitm1:amd64 (14.1.0-1ubuntu1) ... 484s Setting up liblapack3:amd64 (3.12.0-3build1) ... 484s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 484s Setting up cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 484s Setting up python3-numpy (1:1.26.4+ds-10) ... 486s Setting up libgcc-13-dev:amd64 (13.2.0-23ubuntu4) ... 486s Setting up libstdc++-13-dev:amd64 (13.2.0-23ubuntu4) ... 486s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 486s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 486s Setting up python3-scipy (1.11.4-10) ... 490s Setting up cpp-13 (13.2.0-23ubuntu4) ... 490s Setting up gcc-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 490s Setting up gcc-13 (13.2.0-23ubuntu4) ... 490s Setting up cpp (4:13.2.0-7ubuntu1) ... 490s Setting up python3-pymbar (3.1.0-4) ... 490s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 490s """A function that when zeroed is equivalent to the solution of 490s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 490s """ 490s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 490s """ 490s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 490s """ 490s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 490s """ 490s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 490s """ 490s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 490s """Compute estimate of overlap matrix between the states. 490s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 490s """Compute the free energy of occupying a number of bins. 490s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 490s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 490s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 490s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 490s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 490s """ 490s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 490s """Generate samples from forward and reverse Gaussian work distributions. 490s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 490s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 490s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 490s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 490s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 490s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 490s Setting up g++-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... 490s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 490s Setting up gcc (4:13.2.0-7ubuntu1) ... 490s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 490s Setting up g++-13 (13.2.0-23ubuntu4) ... 490s Setting up g++ (4:13.2.0-7ubuntu1) ... 490s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 490s Setting up build-essential (12.10ubuntu1) ... 490s Processing triggers for man-db (2.12.1-1) ... 491s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 491s Reading package lists... 492s Building dependency tree... 492s Reading state information... 492s Starting pkgProblemResolver with broken count: 0 492s Starting 2 pkgProblemResolver with broken count: 0 492s Done 493s The following NEW packages will be installed: 493s autopkgtest-satdep 493s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 493s Need to get 0 B/700 B of archives. 493s After this operation, 0 B of additional disk space will be used. 493s Get:1 /tmp/autopkgtest.aiNrIp/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 493s Selecting previously unselected package autopkgtest-satdep. 493s (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 ... 77925 files and directories currently installed.) 493s Preparing to unpack .../4-autopkgtest-satdep.deb ... 493s Unpacking autopkgtest-satdep (0) ... 493s Setting up autopkgtest-satdep (0) ... 493s autopkgtest: WARNING: package python3-pymbar:i386 is not installed though it should be 495s (Reading database ... 77925 files and directories currently installed.) 495s Removing autopkgtest-satdep (0) ... 497s autopkgtest [01:22:55]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pymbar; print(pymbar)" ; done 497s autopkgtest [01:22:55]: test autodep8-python3: [----------------------- 497s Testing with python3.12: 497s 498s autopkgtest [01:22:56]: test autodep8-python3: -----------------------] 498s autodep8-python3 PASS (superficial) 498s autopkgtest [01:22:56]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 498s autopkgtest [01:22:56]: @@@@@@@@@@@@@@@@@@@@ summary 498s command1 PASS 498s autodep8-python3 PASS (superficial) 509s nova [W] Skipping flock for amd64 509s Creating nova instance adt-oracular-i386-python-pymbar-20240608-011438-juju-7f2275-prod-proposed-migration-environment-3-afd6cc12-23f0-41c6-bbe6-b87bdb2c24a2 from image adt/ubuntu-oracular-amd64-server-20240608.img (UUID c584088c-c855-4ca6-a835-cbd91bb3089c)... 509s nova [W] Skipping flock for amd64 509s Creating nova instance adt-oracular-i386-python-pymbar-20240608-011438-juju-7f2275-prod-proposed-migration-environment-3-afd6cc12-23f0-41c6-bbe6-b87bdb2c24a2 from image adt/ubuntu-oracular-amd64-server-20240608.img (UUID c584088c-c855-4ca6-a835-cbd91bb3089c)...