0s autopkgtest [19:28:35]: starting date and time: 2025-10-28 19:28:35+0000 0s autopkgtest [19:28:35]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [19:28:35]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p8r8zcmx/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:node-jquery --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- lxd -r lxd-armhf-10.145.243.232 lxd-armhf-10.145.243.232:autopkgtest/ubuntu/resolute/armhf 20s autopkgtest [19:28:55]: testbed dpkg architecture: armhf 22s autopkgtest [19:28:57]: testbed apt version: 3.1.6ubuntu2 26s autopkgtest [19:29:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [19:29:03]: testbed release detected to be: None 36s autopkgtest [19:29:10]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 37s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [87.8 kB] 38s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [87.8 kB] 38s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [87.8 kB] 38s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [69.1 kB] 38s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3552 kB] 38s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [194 kB] 38s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 38s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [214 kB] 38s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 38s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1753 kB] 39s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [19.3 kB] 39s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1399 kB] 39s Get:14 http://ftpmaster.internal/ubuntu resolute/restricted Sources [12.5 kB] 39s Get:15 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [308 kB] 39s Get:16 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.0 MB] 40s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1372 kB] 40s Get:18 http://ftpmaster.internal/ubuntu resolute/restricted armhf Packages [1232 B] 40s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.4 MB] 41s Get:20 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [182 kB] 43s Fetched 45.9 MB in 6s (7264 kB/s) 45s Reading package lists... 51s autopkgtest [19:29:26]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Calculating upgrade... 53s The following NEW packages will be installed: 53s python3.14-gdbm 53s The following packages will be upgraded: 53s apparmor apt base-files bind9-dnsutils bind9-host bind9-libs binutils 53s binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils 53s cloud-init cloud-init-base distro-info-data dpkg dpkg-dev eject fdisk 53s gcc-15-base gir1.2-girepository-2.0 gir1.2-glib-2.0 gnu-coreutils 53s libapparmor1 libapt-pkg7.0 libatomic1 libaudit-common libaudit1 libbinutils 53s libblkid1 libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 libdpkg-perl 53s libdrm-common libdrm2 libelf1t64 libfdisk1 libgcc-s1 libgirepository-1.0-1 53s libglib2.0-0t64 libglib2.0-data libjson-c5 liblastlog2-2 libmount1 53s libnewt0.52 libnftables1 libp11-kit0 libpython3.13-minimal 53s libpython3.13-stdlib libseccomp2 libselinux1 libsemanage-common libsemanage2 53s libsframe2 libsmartcols1 libstdc++6 libuuid1 libxml2-16 login 53s lto-disabled-list mount nftables python-apt-common python3-apt 53s python3-bcrypt python3-cffi-backend python3-dbus python3-gdbm 53s python3-inflect python3-jwt python3-markupsafe python3-oauthlib 53s python3-openssl python3-pyparsing python3-yaml python3-zipp python3.13 53s python3.13-gdbm python3.13-minimal sudo-rs tzdata util-linux uuid-runtime 53s whiptail 54s 85 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 26.1 MB of archives. 54s After this operation, 1018 kB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf base-files armhf 14ubuntu4 [75.4 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libatomic1 armhf 15.2.0-5ubuntu1 [7942 B] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-base armhf 15.2.0-5ubuntu1 [58.1 kB] 54s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-s1 armhf 15.2.0-5ubuntu1 [40.6 kB] 54s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++6 armhf 15.2.0-5ubuntu1 [731 kB] 54s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libapt-pkg7.0 armhf 3.1.11 [1157 kB] 54s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg armhf 1.22.21ubuntu4 [1245 kB] 54s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf eject armhf 2.41.2-4ubuntu1 [65.9 kB] 54s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf fdisk armhf 2.41.2-4ubuntu1 [164 kB] 54s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libblkid1 armhf 2.41.2-4ubuntu1 [174 kB] 54s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libmount1 armhf 2.41.2-4ubuntu1 [206 kB] 54s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libsmartcols1 armhf 2.41.2-4ubuntu1 [143 kB] 54s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf mount armhf 2.41.2-4ubuntu1 [166 kB] 54s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf uuid-runtime armhf 2.41.2-4ubuntu1 [67.6 kB] 54s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libuuid1 armhf 2.41.2-4ubuntu1 [43.8 kB] 54s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libfdisk1 armhf 2.41.2-4ubuntu1 [222 kB] 54s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf bsdutils armhf 1:2.41.2-4ubuntu1 [98.2 kB] 54s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf util-linux armhf 2.41.2-4ubuntu1 [1146 kB] 54s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf bsdextrautils armhf 2.41.2-4ubuntu1 [101 kB] 54s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libselinux1 armhf 3.8.1-1build2 [81.3 kB] 54s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libseccomp2 armhf 2.6.0-2ubuntu3 [53.5 kB] 54s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf apt armhf 3.1.11 [1434 kB] 54s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf gnu-coreutils armhf 9.7-3ubuntu1 [1209 kB] 54s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit-common all 1:4.0.5-1build2 [6596 B] 54s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libcap-ng0 armhf 0.8.5-4build3 [14.0 kB] 54s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit1 armhf 1:4.0.5-1build2 [51.7 kB] 54s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf login armhf 1:4.16.0-2+really2.41.2-4ubuntu1 [109 kB] 54s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13 armhf 3.13.9-1 [753 kB] 54s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-minimal armhf 3.13.9-1 [2058 kB] 55s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-stdlib armhf 3.13.9-1 [1957 kB] 55s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.13-minimal armhf 3.13.9-1 [873 kB] 55s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf tzdata all 2025b-5ubuntu1 [198 kB] 55s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf liblastlog2-2 armhf 2.41.2-4ubuntu1 [34.6 kB] 55s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage-common all 3.8.1-1build1 [7916 B] 55s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage2 armhf 3.8.1-1build1 [89.2 kB] 55s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf distro-info-data all 0.68 [7378 B] 55s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-girepository-2.0 armhf 1.86.0-6 [25.3 kB] 55s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-glib-2.0 armhf 2.86.1-1 [182 kB] 55s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libglib2.0-0t64 armhf 2.86.1-1 [1482 kB] 55s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libgirepository-1.0-1 armhf 1.86.0-6 [111 kB] 55s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libapparmor1 armhf 5.0.0~alpha1-0ubuntu8.1 [52.9 kB] 55s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libelf1t64 armhf 0.193-3 [50.9 kB] 55s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libglib2.0-data all 2.86.1-1 [56.7 kB] 55s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-c5 armhf 0.18+ds-1.1 [33.3 kB] 55s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libnewt0.52 armhf 0.52.25-1ubuntu2 [39.9 kB] 55s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libp11-kit0 armhf 0.25.9-2 [265 kB] 55s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libxml2-16 armhf 2.14.5+dfsg-0.2build1 [527 kB] 55s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf python-apt-common all 3.0.0ubuntu2 [21.7 kB] 55s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf python3-apt armhf 3.0.0ubuntu2 [189 kB] 55s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cffi-backend armhf 2.0.0-2 [99.1 kB] 55s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf python3-dbus armhf 1.4.0-1build1 [113 kB] 55s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf python3-yaml armhf 6.0.2-2 [181 kB] 55s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf sudo-rs armhf 0.2.8-1ubuntu5.1 [548 kB] 55s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf whiptail armhf 0.52.25-1ubuntu2 [17.1 kB] 55s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf apparmor armhf 5.0.0~alpha1-0ubuntu8.1 [631 kB] 55s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-dnsutils armhf 1:9.20.11-1ubuntu3 [156 kB] 55s Get:57 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-host armhf 1:9.20.11-1ubuntu3 [46.5 kB] 55s Get:58 http://ftpmaster.internal/ubuntu resolute/main armhf bind9-libs armhf 1:9.20.11-1ubuntu3 [1202 kB] 55s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm-common all 2.4.127-1ubuntu1 [9716 B] 55s Get:60 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm2 armhf 2.4.127-1ubuntu1 [37.8 kB] 55s Get:61 http://ftpmaster.internal/ubuntu resolute/main armhf nftables armhf 1.1.5-2 [73.2 kB] 55s Get:62 http://ftpmaster.internal/ubuntu resolute/main armhf libnftables1 armhf 1.1.5-2 [329 kB] 55s Get:63 http://ftpmaster.internal/ubuntu resolute/main armhf python3.13-gdbm armhf 3.13.9-1 [30.9 kB] 55s Get:64 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-gdbm armhf 3.14.0-4 [31.3 kB] 55s Get:65 http://ftpmaster.internal/ubuntu resolute/main armhf python3-gdbm armhf 3.13.9-1 [8884 B] 55s Get:66 http://ftpmaster.internal/ubuntu resolute/main armhf libctf0 armhf 2.45-8ubuntu1 [75.7 kB] 55s Get:67 http://ftpmaster.internal/ubuntu resolute/main armhf libctf-nobfd0 armhf 2.45-8ubuntu1 [78.9 kB] 55s Get:68 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-arm-linux-gnueabihf armhf 2.45-8ubuntu1 [1022 kB] 55s Get:69 http://ftpmaster.internal/ubuntu resolute/main armhf libbinutils armhf 2.45-8ubuntu1 [411 kB] 55s Get:70 http://ftpmaster.internal/ubuntu resolute/main armhf binutils armhf 2.45-8ubuntu1 [3234 B] 55s Get:71 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-common armhf 2.45-8ubuntu1 [221 kB] 55s Get:72 http://ftpmaster.internal/ubuntu resolute/main armhf libsframe2 armhf 2.45-8ubuntu1 [13.3 kB] 55s Get:73 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB] 55s Get:74 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B] 55s Get:75 http://ftpmaster.internal/ubuntu resolute/main armhf python3-jwt all 2.10.1-3 [21.1 kB] 55s Get:76 http://ftpmaster.internal/ubuntu resolute/main armhf python3-oauthlib all 3.3.1-1 [93.5 kB] 55s Get:77 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg-dev all 1.22.21ubuntu4 [1088 kB] 55s Get:78 http://ftpmaster.internal/ubuntu resolute/main armhf libdpkg-perl all 1.22.21ubuntu4 [280 kB] 55s Get:79 http://ftpmaster.internal/ubuntu resolute/main armhf lto-disabled-list all 71 [12.5 kB] 55s Get:80 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.1.0-2build6 [320 kB] 55s Get:81 http://ftpmaster.internal/ubuntu resolute/main armhf python3-inflect all 7.5.0-1 [33.9 kB] 55s Get:82 http://ftpmaster.internal/ubuntu resolute/main armhf python3-markupsafe armhf 2.1.5-1build5 [13.3 kB] 55s Get:83 http://ftpmaster.internal/ubuntu resolute/main armhf python3-openssl all 25.1.0-1 [46.4 kB] 55s Get:84 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pyparsing all 3.1.3-1 [87.0 kB] 55s Get:85 http://ftpmaster.internal/ubuntu resolute/main armhf python3-zipp all 3.23.0-1 [10.4 kB] 55s Get:86 http://ftpmaster.internal/ubuntu resolute/main armhf python3-bcrypt armhf 4.3.0-2 [251 kB] 56s Preconfiguring packages ... 56s Fetched 26.1 MB in 2s (12.4 MB/s) 56s (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 ... 61081 files and directories currently installed.) 56s Preparing to unpack .../base-files_14ubuntu4_armhf.deb ... 56s Unpacking base-files (14ubuntu4) over (14ubuntu3) ... 56s Setting up base-files (14ubuntu4) ... 56s Installing new version of config file /etc/issue ... 56s Installing new version of config file /etc/issue.net ... 56s Installing new version of config file /etc/lsb-release ... 57s motd-news.service is a disabled or a static unit not running, not starting it. 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libatomic1_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking libatomic1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Preparing to unpack .../gcc-15-base_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking gcc-15-base:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up gcc-15-base:armhf (15.2.0-5ubuntu1) ... 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libgcc-s1_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking libgcc-s1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up libgcc-s1:armhf (15.2.0-5ubuntu1) ... 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libstdc++6_15.2.0-5ubuntu1_armhf.deb ... 57s Unpacking libstdc++6:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 57s Setting up libstdc++6:armhf (15.2.0-5ubuntu1) ... 57s (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 ... 61081 files and directories currently installed.) 57s Preparing to unpack .../libapt-pkg7.0_3.1.11_armhf.deb ... 57s Unpacking libapt-pkg7.0:armhf (3.1.11) over (3.1.6ubuntu2) ... 58s Setting up libapt-pkg7.0:armhf (3.1.11) ... 58s (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 ... 61082 files and directories currently installed.) 58s Preparing to unpack .../dpkg_1.22.21ubuntu4_armhf.deb ... 58s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 58s Setting up dpkg (1.22.21ubuntu4) ... 58s (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 ... 61082 files and directories currently installed.) 58s Preparing to unpack .../eject_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking eject (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Preparing to unpack .../fdisk_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking fdisk (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Preparing to unpack .../libblkid1_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking libblkid1:armhf (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Setting up libblkid1:armhf (2.41.2-4ubuntu1) ... 58s (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 ... 61082 files and directories currently installed.) 58s Preparing to unpack .../libmount1_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking libmount1:armhf (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Setting up libmount1:armhf (2.41.2-4ubuntu1) ... 58s (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 ... 61082 files and directories currently installed.) 58s Preparing to unpack .../libsmartcols1_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking libsmartcols1:armhf (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Setting up libsmartcols1:armhf (2.41.2-4ubuntu1) ... 58s (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 ... 61082 files and directories currently installed.) 58s Preparing to unpack .../mount_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking mount (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Preparing to unpack .../uuid-runtime_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking uuid-runtime (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 58s Preparing to unpack .../libuuid1_2.41.2-4ubuntu1_armhf.deb ... 58s Unpacking libuuid1:armhf (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 59s Setting up libuuid1:armhf (2.41.2-4ubuntu1) ... 59s (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 ... 61082 files and directories currently installed.) 59s Preparing to unpack .../libfdisk1_2.41.2-4ubuntu1_armhf.deb ... 59s Unpacking libfdisk1:armhf (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 59s Preparing to unpack .../bsdutils_1%3a2.41.2-4ubuntu1_armhf.deb ... 59s Unpacking bsdutils (1:2.41.2-4ubuntu1) over (1:2.41-4ubuntu4) ... 59s Setting up bsdutils (1:2.41.2-4ubuntu1) ... 59s (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 ... 61079 files and directories currently installed.) 59s Preparing to unpack .../util-linux_2.41.2-4ubuntu1_armhf.deb ... 59s Unpacking util-linux (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 59s Setting up util-linux (2.41.2-4ubuntu1) ... 59s fstrim.service is a disabled or a static unit not running, not starting it. 60s (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 ... 61050 files and directories currently installed.) 60s Preparing to unpack .../bsdextrautils_2.41.2-4ubuntu1_armhf.deb ... 60s Unpacking bsdextrautils (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 60s Preparing to unpack .../libselinux1_3.8.1-1build2_armhf.deb ... 60s Unpacking libselinux1:armhf (3.8.1-1build2) over (3.8.1-1build1) ... 60s Setting up libselinux1:armhf (3.8.1-1build2) ... 60s (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 ... 61053 files and directories currently installed.) 60s Preparing to unpack .../libseccomp2_2.6.0-2ubuntu3_armhf.deb ... 60s Unpacking libseccomp2:armhf (2.6.0-2ubuntu3) over (2.6.0-2ubuntu2) ... 60s Setting up libseccomp2:armhf (2.6.0-2ubuntu3) ... 60s (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 ... 61053 files and directories currently installed.) 60s Preparing to unpack .../archives/apt_3.1.11_armhf.deb ... 60s Unpacking apt (3.1.11) over (3.1.6ubuntu2) ... 60s Setting up apt (3.1.11) ... 60s Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... 61s (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 ... 61054 files and directories currently installed.) 61s Preparing to unpack .../gnu-coreutils_9.7-3ubuntu1_armhf.deb ... 61s Unpacking gnu-coreutils (9.7-3ubuntu1) over (9.5-1ubuntu4) ... 61s Setting up gnu-coreutils (9.7-3ubuntu1) ... 61s (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 ... 61049 files and directories currently installed.) 61s Preparing to unpack .../libaudit-common_1%3a4.0.5-1build2_all.deb ... 61s Unpacking libaudit-common (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 61s Setting up libaudit-common (1:4.0.5-1build2) ... 61s (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 ... 61049 files and directories currently installed.) 61s Preparing to unpack .../libcap-ng0_0.8.5-4build3_armhf.deb ... 61s Unpacking libcap-ng0:armhf (0.8.5-4build3) over (0.8.5-4build2) ... 61s Setting up libcap-ng0:armhf (0.8.5-4build3) ... 61s (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 ... 61049 files and directories currently installed.) 61s Preparing to unpack .../libaudit1_1%3a4.0.5-1build2_armhf.deb ... 61s Unpacking libaudit1:armhf (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 61s Setting up libaudit1:armhf (1:4.0.5-1build2) ... 61s (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 ... 61049 files and directories currently installed.) 61s Preparing to unpack .../0-login_1%3a4.16.0-2+really2.41.2-4ubuntu1_armhf.deb ... 61s Unpacking login (1:4.16.0-2+really2.41.2-4ubuntu1) over (1:4.16.0-2+really2.41-4ubuntu4) ... 61s Preparing to unpack .../1-python3.13_3.13.9-1_armhf.deb ... 61s Unpacking python3.13 (3.13.9-1) over (3.13.7-1) ... 61s Preparing to unpack .../2-python3.13-minimal_3.13.9-1_armhf.deb ... 61s Unpacking python3.13-minimal (3.13.9-1) over (3.13.7-1) ... 61s Preparing to unpack .../3-libpython3.13-stdlib_3.13.9-1_armhf.deb ... 61s Unpacking libpython3.13-stdlib:armhf (3.13.9-1) over (3.13.7-1) ... 61s Preparing to unpack .../4-libpython3.13-minimal_3.13.9-1_armhf.deb ... 61s Unpacking libpython3.13-minimal:armhf (3.13.9-1) over (3.13.7-1) ... 62s Preparing to unpack .../5-tzdata_2025b-5ubuntu1_all.deb ... 62s Unpacking tzdata (2025b-5ubuntu1) over (2025b-3ubuntu1) ... 62s Preparing to unpack .../6-liblastlog2-2_2.41.2-4ubuntu1_armhf.deb ... 62s Unpacking liblastlog2-2:armhf (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 62s Setting up liblastlog2-2:armhf (2.41.2-4ubuntu1) ... 62s (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 ... 61041 files and directories currently installed.) 62s Preparing to unpack .../libsemanage-common_3.8.1-1build1_all.deb ... 62s Unpacking libsemanage-common (3.8.1-1build1) over (3.8.1-1) ... 62s Setting up libsemanage-common (3.8.1-1build1) ... 62s (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 ... 61041 files and directories currently installed.) 62s Preparing to unpack .../libsemanage2_3.8.1-1build1_armhf.deb ... 62s Unpacking libsemanage2:armhf (3.8.1-1build1) over (3.8.1-1) ... 62s Setting up libsemanage2:armhf (3.8.1-1build1) ... 62s (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 ... 61041 files and directories currently installed.) 62s Preparing to unpack .../00-distro-info-data_0.68_all.deb ... 62s Unpacking distro-info-data (0.68) over (0.66) ... 62s Preparing to unpack .../01-gir1.2-girepository-2.0_1.86.0-6_armhf.deb ... 62s Unpacking gir1.2-girepository-2.0:armhf (1.86.0-6) over (1.84.0-1) ... 62s Preparing to unpack .../02-gir1.2-glib-2.0_2.86.1-1_armhf.deb ... 62s Unpacking gir1.2-glib-2.0:armhf (2.86.1-1) over (2.86.0-2) ... 62s Preparing to unpack .../03-libglib2.0-0t64_2.86.1-1_armhf.deb ... 62s Unpacking libglib2.0-0t64:armhf (2.86.1-1) over (2.86.0-2) ... 62s Preparing to unpack .../04-libgirepository-1.0-1_1.86.0-6_armhf.deb ... 62s Unpacking libgirepository-1.0-1:armhf (1.86.0-6) over (1.84.0-1) ... 62s Preparing to unpack .../05-libapparmor1_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 62s Unpacking libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 62s Preparing to unpack .../06-libelf1t64_0.193-3_armhf.deb ... 62s Unpacking libelf1t64:armhf (0.193-3) over (0.193-1) ... 62s Preparing to unpack .../07-libglib2.0-data_2.86.1-1_all.deb ... 62s Unpacking libglib2.0-data (2.86.1-1) over (2.86.0-2) ... 62s Preparing to unpack .../08-libjson-c5_0.18+ds-1.1_armhf.deb ... 62s Unpacking libjson-c5:armhf (0.18+ds-1.1) over (0.18+ds-1) ... 62s Preparing to unpack .../09-libnewt0.52_0.52.25-1ubuntu2_armhf.deb ... 62s Unpacking libnewt0.52:armhf (0.52.25-1ubuntu2) over (0.52.25-1ubuntu1) ... 62s Preparing to unpack .../10-libp11-kit0_0.25.9-2_armhf.deb ... 62s Unpacking libp11-kit0:armhf (0.25.9-2) over (0.25.5-3ubuntu1) ... 62s Preparing to unpack .../11-libxml2-16_2.14.5+dfsg-0.2build1_armhf.deb ... 62s Unpacking libxml2-16:armhf (2.14.5+dfsg-0.2build1) over (2.14.5+dfsg-0.2) ... 62s Preparing to unpack .../12-python-apt-common_3.0.0ubuntu2_all.deb ... 62s Unpacking python-apt-common (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 62s Preparing to unpack .../13-python3-apt_3.0.0ubuntu2_armhf.deb ... 63s Unpacking python3-apt (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 63s Preparing to unpack .../14-python3-cffi-backend_2.0.0-2_armhf.deb ... 63s Unpacking python3-cffi-backend:armhf (2.0.0-2) over (1.17.1-3) ... 63s Preparing to unpack .../15-python3-dbus_1.4.0-1build1_armhf.deb ... 63s Unpacking python3-dbus (1.4.0-1build1) over (1.4.0-1) ... 63s Preparing to unpack .../16-python3-yaml_6.0.2-2_armhf.deb ... 63s Unpacking python3-yaml (6.0.2-2) over (6.0.2-1build2) ... 63s Preparing to unpack .../17-sudo-rs_0.2.8-1ubuntu5.1_armhf.deb ... 63s Unpacking sudo-rs (0.2.8-1ubuntu5.1) over (0.2.8-1ubuntu5) ... 63s Preparing to unpack .../18-whiptail_0.52.25-1ubuntu2_armhf.deb ... 63s Unpacking whiptail (0.52.25-1ubuntu2) over (0.52.25-1ubuntu1) ... 63s Preparing to unpack .../19-apparmor_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 64s Unpacking apparmor (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 65s Preparing to unpack .../20-bind9-dnsutils_1%3a9.20.11-1ubuntu3_armhf.deb ... 65s Unpacking bind9-dnsutils (1:9.20.11-1ubuntu3) over (1:9.20.11-1ubuntu2) ... 65s Preparing to unpack .../21-bind9-host_1%3a9.20.11-1ubuntu3_armhf.deb ... 65s Unpacking bind9-host (1:9.20.11-1ubuntu3) over (1:9.20.11-1ubuntu2) ... 65s Preparing to unpack .../22-bind9-libs_1%3a9.20.11-1ubuntu3_armhf.deb ... 65s Unpacking bind9-libs:armhf (1:9.20.11-1ubuntu3) over (1:9.20.11-1ubuntu2) ... 65s Preparing to unpack .../23-libdrm-common_2.4.127-1ubuntu1_all.deb ... 65s Unpacking libdrm-common (2.4.127-1ubuntu1) over (2.4.125-1) ... 65s Preparing to unpack .../24-libdrm2_2.4.127-1ubuntu1_armhf.deb ... 65s Unpacking libdrm2:armhf (2.4.127-1ubuntu1) over (2.4.125-1) ... 65s Preparing to unpack .../25-nftables_1.1.5-2_armhf.deb ... 65s Unpacking nftables (1.1.5-2) over (1.1.5-1) ... 65s Preparing to unpack .../26-libnftables1_1.1.5-2_armhf.deb ... 65s Unpacking libnftables1:armhf (1.1.5-2) over (1.1.5-1) ... 65s Preparing to unpack .../27-python3.13-gdbm_3.13.9-1_armhf.deb ... 65s Unpacking python3.13-gdbm (3.13.9-1) over (3.13.7-1) ... 65s Selecting previously unselected package python3.14-gdbm. 65s Preparing to unpack .../28-python3.14-gdbm_3.14.0-4_armhf.deb ... 65s Unpacking python3.14-gdbm (3.14.0-4) ... 65s Preparing to unpack .../29-python3-gdbm_3.13.9-1_armhf.deb ... 65s Unpacking python3-gdbm:armhf (3.13.9-1) over (3.13.5-1) ... 65s Preparing to unpack .../30-libctf0_2.45-8ubuntu1_armhf.deb ... 65s Unpacking libctf0:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../31-libctf-nobfd0_2.45-8ubuntu1_armhf.deb ... 65s Unpacking libctf-nobfd0:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../32-binutils-arm-linux-gnueabihf_2.45-8ubuntu1_armhf.deb ... 65s Unpacking binutils-arm-linux-gnueabihf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../33-libbinutils_2.45-8ubuntu1_armhf.deb ... 65s Unpacking libbinutils:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../34-binutils_2.45-8ubuntu1_armhf.deb ... 65s Unpacking binutils (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../35-binutils-common_2.45-8ubuntu1_armhf.deb ... 65s Unpacking binutils-common:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../36-libsframe2_2.45-8ubuntu1_armhf.deb ... 65s Unpacking libsframe2:armhf (2.45-8ubuntu1) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../37-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ... 66s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 66s Preparing to unpack .../38-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ... 66s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 66s Preparing to unpack .../39-python3-jwt_2.10.1-3_all.deb ... 66s Unpacking python3-jwt (2.10.1-3) over (2.10.1-2) ... 66s Preparing to unpack .../40-python3-oauthlib_3.3.1-1_all.deb ... 66s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 66s Preparing to unpack .../41-dpkg-dev_1.22.21ubuntu4_all.deb ... 66s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 66s Preparing to unpack .../42-libdpkg-perl_1.22.21ubuntu4_all.deb ... 66s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 66s Preparing to unpack .../43-lto-disabled-list_71_all.deb ... 66s Unpacking lto-disabled-list (71) over (69) ... 66s Preparing to unpack .../44-libbrotli1_1.1.0-2build6_armhf.deb ... 66s Unpacking libbrotli1:armhf (1.1.0-2build6) over (1.1.0-2build5) ... 66s Preparing to unpack .../45-python3-inflect_7.5.0-1_all.deb ... 66s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 66s Preparing to unpack .../46-python3-markupsafe_2.1.5-1build5_armhf.deb ... 66s Unpacking python3-markupsafe (2.1.5-1build5) over (2.1.5-1build4) ... 66s Preparing to unpack .../47-python3-openssl_25.1.0-1_all.deb ... 67s Unpacking python3-openssl (25.1.0-1) over (25.0.0-1) ... 67s Preparing to unpack .../48-python3-pyparsing_3.1.3-1_all.deb ... 67s Unpacking python3-pyparsing (3.1.3-1) over (3.1.2-1) ... 67s Preparing to unpack .../49-python3-zipp_3.23.0-1_all.deb ... 67s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 67s Preparing to unpack .../50-python3-bcrypt_4.3.0-2_armhf.deb ... 67s Unpacking python3-bcrypt (4.3.0-2) over (4.2.0-2.1build1) ... 67s Setting up lto-disabled-list (71) ... 67s Setting up libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) ... 67s Setting up libnewt0.52:armhf (0.52.25-1ubuntu2) ... 67s Setting up libnftables1:armhf (1.1.5-2) ... 67s Setting up nftables (1.1.5-2) ... 67s Setting up bsdextrautils (2.41.2-4ubuntu1) ... 67s Setting up python3-jwt (2.10.1-3) ... 67s Setting up distro-info-data (0.68) ... 67s Setting up libxml2-16:armhf (2.14.5+dfsg-0.2build1) ... 67s Setting up libsframe2:armhf (2.45-8ubuntu1) ... 67s Setting up python3-openssl (25.1.0-1) ... 68s Setting up python3-bcrypt (4.3.0-2) ... 68s Setting up libbrotli1:armhf (1.1.0-2build6) ... 68s Setting up binutils-common:armhf (2.45-8ubuntu1) ... 68s Setting up libctf-nobfd0:armhf (2.45-8ubuntu1) ... 68s Setting up python3-yaml (6.0.2-2) ... 68s Setting up python3-zipp (3.23.0-1) ... 68s Setting up python3-markupsafe (2.1.5-1build5) ... 68s Setting up libelf1t64:armhf (0.193-3) ... 68s Setting up tzdata (2025b-5ubuntu1) ... 68s 68s Current default time zone: 'Etc/UTC' 68s Local time is now: Tue Oct 28 19:29:43 UTC 2025. 68s Universal Time is now: Tue Oct 28 19:29:43 UTC 2025. 68s Run 'dpkg-reconfigure tzdata' if you wish to change it. 68s 68s Setting up eject (2.41.2-4ubuntu1) ... 68s Setting up libpython3.13-minimal:armhf (3.13.9-1) ... 68s Setting up apparmor (5.0.0~alpha1-0ubuntu8.1) ... 68s Installing new version of config file /etc/apparmor.d/fusermount3 ... 68s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 68s 68s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 68s 68s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 68s 69s Reloading AppArmor profiles 69s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "bwrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "babeld". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "bgpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "bfdd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "alsamixer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "dnstracer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "eigrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "fabricd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "dig". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "hostname". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "iotop-c". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "fusermount3". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 70s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ldpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "john". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "gs". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Unable to replace "isisd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Unable to replace "linux-boot-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "irssi". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lsblk". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lsusb". /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "compressor". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "locale". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mosquitto". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mbsync". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Unable to replace "nhrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "nslookup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "nc.openbsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "notify-send". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ospf6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "os-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pbrd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pim6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Unable to replace "pathd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Unable to replace "ospfd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pimd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qpdf". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ripd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ripngd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "openvpn". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "proftpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "staticd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "systemd-detect-virt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tinyproxy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ssh-keyscan". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mx-extract". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rygel". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "/usr/sbin/chronyd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "cmds". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tnftp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "dumpcap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "who". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vrrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wg-quick". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "znc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s Error: At least one profile failed to load 70s Setting up python3-inflect (7.5.0-1) ... 70s Setting up libglib2.0-data (2.86.1-1) ... 70s Setting up python3-oauthlib (3.3.1-1) ... 70s Setting up python3-pyparsing (3.1.3-1) ... 70s Setting up python3.14-gdbm (3.14.0-4) ... 70s Setting up libp11-kit0:armhf (0.25.9-2) ... 70s Setting up libatomic1:armhf (15.2.0-5ubuntu1) ... 70s Setting up libdpkg-perl (1.22.21ubuntu4) ... 70s Setting up libfdisk1:armhf (2.41.2-4ubuntu1) ... 70s Setting up whiptail (0.52.25-1ubuntu2) ... 70s Setting up python-apt-common (3.0.0ubuntu2) ... 70s Setting up mount (2.41.2-4ubuntu1) ... 70s Setting up uuid-runtime (2.41.2-4ubuntu1) ... 71s uuidd.service is a disabled or a static unit not running, not starting it. 71s Setting up python3.13-minimal (3.13.9-1) ... 72s Setting up libbinutils:armhf (2.45-8ubuntu1) ... 72s Setting up libdrm-common (2.4.127-1ubuntu1) ... 72s Setting up libpython3.13-stdlib:armhf (3.13.9-1) ... 72s Setting up libjson-c5:armhf (0.18+ds-1.1) ... 72s Setting up sudo-rs (0.2.8-1ubuntu5.1) ... 72s Setting up python3-cffi-backend:armhf (2.0.0-2) ... 72s Setting up python3.13-gdbm (3.13.9-1) ... 72s Setting up login (1:4.16.0-2+really2.41.2-4ubuntu1) ... 72s Setting up libctf0:armhf (2.45-8ubuntu1) ... 72s Setting up bind9-libs:armhf (1:9.20.11-1ubuntu3) ... 72s Setting up python3.13 (3.13.9-1) ... 73s Setting up python3-gdbm:armhf (3.13.9-1) ... 73s Setting up python3-apt (3.0.0ubuntu2) ... 73s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ... 73s Encountered debconf setting for cloud-init-base/datasources. 75s Setting up fdisk (2.41.2-4ubuntu1) ... 75s Setting up libglib2.0-0t64:armhf (2.86.1-1) ... 75s No schema files found: doing nothing. 75s Setting up gir1.2-glib-2.0:armhf (2.86.1-1) ... 75s Setting up libdrm2:armhf (2.4.127-1ubuntu1) ... 75s Setting up libgirepository-1.0-1:armhf (1.86.0-6) ... 75s Setting up bind9-host (1:9.20.11-1ubuntu3) ... 75s Setting up binutils-arm-linux-gnueabihf (2.45-8ubuntu1) ... 75s Setting up python3-dbus (1.4.0-1build1) ... 76s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ... 76s Setting up binutils (2.45-8ubuntu1) ... 76s Setting up dpkg-dev (1.22.21ubuntu4) ... 76s Setting up gir1.2-girepository-2.0:armhf (1.86.0-6) ... 76s Setting up bind9-dnsutils (1:9.20.11-1ubuntu3) ... 76s Processing triggers for libc-bin (2.42-0ubuntu3) ... 76s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 76s Processing triggers for systemd (257.9-0ubuntu2) ... 76s Processing triggers for man-db (2.13.1-1) ... 78s Processing triggers for plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu1) ... 78s Processing triggers for procps (2:4.0.4-8ubuntu3) ... 78s Processing triggers for install-info (7.1.1-1ubuntu1) ... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Solving dependencies... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [19:29:59]: rebooting testbed after setup commands that affected boot 125s autopkgtest [19:30:40]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 149s autopkgtest [19:31:04]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 170s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 170s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 170s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 170s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 170s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 170s gpgv: Can't check signature: No public key 170s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 171s autopkgtest [19:31:26]: testing package pdb2pqr version 3.6.1+dfsg-1 173s autopkgtest [19:31:28]: build not needed 177s autopkgtest [19:31:32]: test installation-test: preparing testbed 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Solving dependencies... 180s The following NEW packages will be installed: 180s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 180s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 180s python3-roman sgml-base xml-core 181s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 7246 kB of archives. 181s After this operation, 28.4 MB of additional disk space will be used. 181s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 181s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-6build1 [133 kB] 181s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-5ubuntu1 [334 kB] 181s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-6build1 [2091 kB] 181s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 182s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 182s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19 [20.3 kB] 182s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 182s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf python3-roman all 5.1-1 [10.6 kB] 182s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 182s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pdbx all 2.0.1-2 [16.5 kB] 182s Get:12 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-propka all 3.5.1-2 [70.1 kB] 182s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 182s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 182s Fetched 7246 kB in 1s (5134 kB/s) 182s Selecting previously unselected package python3-numpy-dev:armhf. 182s (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 ... 61068 files and directories currently installed.) 182s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 182s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 182s Selecting previously unselected package libblas3:armhf. 182s Preparing to unpack .../01-libblas3_3.12.1-6build1_armhf.deb ... 182s Unpacking libblas3:armhf (3.12.1-6build1) ... 182s Selecting previously unselected package libgfortran5:armhf. 182s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_armhf.deb ... 182s Unpacking libgfortran5:armhf (15.2.0-5ubuntu1) ... 182s Selecting previously unselected package liblapack3:armhf. 182s Preparing to unpack .../03-liblapack3_3.12.1-6build1_armhf.deb ... 182s Unpacking liblapack3:armhf (3.12.1-6build1) ... 183s Selecting previously unselected package python3-numpy. 183s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 183s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 183s Selecting previously unselected package sgml-base. 183s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 183s Unpacking sgml-base (1.31+nmu1) ... 183s Selecting previously unselected package xml-core. 183s Preparing to unpack .../06-xml-core_0.19_all.deb ... 183s Unpacking xml-core (0.19) ... 183s Selecting previously unselected package docutils-common. 183s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 183s Unpacking docutils-common (0.21.2+dfsg-2) ... 183s Selecting previously unselected package python3-roman. 183s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 183s Unpacking python3-roman (5.1-1) ... 183s Selecting previously unselected package python3-docutils. 183s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 183s Unpacking python3-docutils (0.21.2+dfsg-2) ... 183s Selecting previously unselected package python3-pdbx. 183s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 183s Unpacking python3-pdbx (2.0.1-2) ... 183s Selecting previously unselected package python3-propka. 183s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 183s Unpacking python3-propka (3.5.1-2) ... 183s Selecting previously unselected package python3-pdb2pqr. 183s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 183s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 183s Selecting previously unselected package pdb2pqr. 183s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 183s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 183s Setting up python3-propka (3.5.1-2) ... 183s Setting up python3-pdbx (2.0.1-2) ... 184s Setting up python3-roman (5.1-1) ... 184s Setting up libblas3:armhf (3.12.1-6build1) ... 184s 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 184s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 184s Setting up libgfortran5:armhf (15.2.0-5ubuntu1) ... 184s Setting up sgml-base (1.31+nmu1) ... 184s Setting up liblapack3:armhf (3.12.1-6build1) ... 184s 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 184s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 186s Setting up xml-core (0.19) ... 186s Processing triggers for libc-bin (2.42-0ubuntu3) ... 186s Processing triggers for man-db (2.13.1-1) ... 186s Processing triggers for sgml-base (1.31+nmu1) ... 186s Setting up docutils-common (0.21.2+dfsg-2) ... 187s Processing triggers for sgml-base (1.31+nmu1) ... 187s Setting up python3-docutils (0.21.2+dfsg-2) ... 187s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 187s Setting up pdb2pqr (3.6.1+dfsg-1) ... 195s autopkgtest [19:31:50]: test installation-test: [----------------------- 197s Run pdb2pqr... 198s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 198s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 198s INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 198s INFO:Checking and transforming input arguments. 198s INFO:Loading topology files. 198s INFO:Loading molecule: examples/1a1p/1a1p.pdb 198s INFO:Setting up molecule. 198s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 198s INFO:Created biomolecule object with 14 residues and 208 atoms. 198s INFO:Setting termini states for biomolecule chains. 198s INFO:Loading forcefield. 198s INFO:Loading hydrogen topology definitions. 198s INFO:This biomolecule is clean. No repair needed. 198s INFO:Updating disulfide bridges. 198s INFO:Debumping biomolecule. 198s INFO:Adding hydrogens to biomolecule. 198s INFO:Debumping biomolecule (again). 198s INFO:Optimizing hydrogen bonds 198s INFO:Applying force field to biomolecule states. 198s INFO:Regenerating headers. 198s INFO:Regenerating PDB lines. 198s WARNING:Ignoring 852 header lines in output. 198s WARNING:Ignoring 3 missing lines in output. 198s autopkgtest [19:31:53]: test installation-test: -----------------------] 203s installation-test PASS 203s autopkgtest [19:31:58]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 208s autopkgtest [19:32:03]: test pdb2pka-test: preparing testbed 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s Solving dependencies... 211s The following NEW packages will be installed: 211s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 211s pdb2pqr-doc sphinx-rtd-theme-common 211s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 5035 kB of archives. 211s After this operation, 20.0 MB of additional disk space will be used. 211s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1 [2781 kB] 212s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 213s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 213s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 213s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 213s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 213s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 213s Fetched 5035 kB in 2s (2235 kB/s) 213s Selecting previously unselected package fonts-lato. 213s (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 ... 62570 files and directories currently installed.) 213s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 213s Unpacking fonts-lato (2.015-1) ... 214s Selecting previously unselected package fonts-font-awesome. 214s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 214s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 214s Selecting previously unselected package libjs-jquery. 214s Preparing to unpack .../2-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 214s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 214s Selecting previously unselected package libjs-underscore. 214s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 214s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 214s Selecting previously unselected package libjs-sphinxdoc. 214s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 214s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 214s Selecting previously unselected package sphinx-rtd-theme-common. 214s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 214s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 214s Selecting previously unselected package pdb2pqr-doc. 214s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 214s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 214s Setting up fonts-lato (2.015-1) ... 214s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 214s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 214s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 214s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 214s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 214s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 229s autopkgtest [19:32:24]: test pdb2pka-test: [----------------------- 231s Run pdb2pqr... 231s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 231s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 231s INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 231s INFO:Checking and transforming input arguments. 231s INFO:Loading topology files. 232s INFO:Loading molecule: 1a1p/1a1p.pdb 232s INFO:Setting up molecule. 232s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 232s INFO:Created biomolecule object with 14 residues and 208 atoms. 232s INFO:Setting termini states for biomolecule chains. 232s INFO:Loading forcefield. 232s INFO:Loading hydrogen topology definitions. 232s INFO:This biomolecule is clean. No repair needed. 232s INFO:Updating disulfide bridges. 232s INFO:Debumping biomolecule. 232s INFO:Adding hydrogens to biomolecule. 232s INFO:Debumping biomolecule (again). 232s INFO:Optimizing hydrogen bonds 232s INFO:Applying force field to biomolecule states. 232s INFO:Regenerating headers. 232s INFO:Regenerating PDB lines. 232s WARNING:Ignoring 852 header lines in output. 232s WARNING:Ignoring 3 missing lines in output. 232s autopkgtest [19:32:27]: test pdb2pka-test: -----------------------] 237s autopkgtest [19:32:32]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 237s pdb2pka-test PASS 242s autopkgtest [19:32:37]: test command1: preparing testbed 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 244s Solving dependencies... 245s The following NEW packages will be installed: 245s python3-dateutil python3-iniconfig python3-packaging python3-pandas 245s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 245s python3-testfixtures 245s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 245s Need to get 11.5 MB of archives. 245s After this operation, 55.7 MB of additional disk space will be used. 245s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-dateutil all 2.9.0-4 [80.3 kB] 246s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 246s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf python3-packaging all 25.0-1 [52.8 kB] 246s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pytz all 2025.2-4 [32.3 kB] 246s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas-lib armhf 2.3.3+dfsg-1ubuntu1 [8020 kB] 251s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 252s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pluggy all 1.6.0-1 [21.0 kB] 252s Get:8 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytest all 8.3.5-2 [252 kB] 252s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-testfixtures all 9.2.0-1 [79.2 kB] 252s Fetched 11.5 MB in 7s (1661 kB/s) 252s Selecting previously unselected package python3-dateutil. 252s (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 ... 62905 files and directories currently installed.) 252s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 252s Unpacking python3-dateutil (2.9.0-4) ... 252s Selecting previously unselected package python3-iniconfig. 252s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 252s Unpacking python3-iniconfig (1.1.1-2) ... 252s Selecting previously unselected package python3-packaging. 252s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 252s Unpacking python3-packaging (25.0-1) ... 252s Selecting previously unselected package python3-pytz. 252s Preparing to unpack .../3-python3-pytz_2025.2-4_all.deb ... 252s Unpacking python3-pytz (2025.2-4) ... 252s Selecting previously unselected package python3-pandas-lib:armhf. 252s Preparing to unpack .../4-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_armhf.deb ... 252s Unpacking python3-pandas-lib:armhf (2.3.3+dfsg-1ubuntu1) ... 253s Selecting previously unselected package python3-pandas. 253s Preparing to unpack .../5-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 253s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 253s Selecting previously unselected package python3-pluggy. 253s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 253s Unpacking python3-pluggy (1.6.0-1) ... 253s Selecting previously unselected package python3-pytest. 253s Preparing to unpack .../7-python3-pytest_8.3.5-2_all.deb ... 253s Unpacking python3-pytest (8.3.5-2) ... 253s Selecting previously unselected package python3-testfixtures. 253s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 253s Unpacking python3-testfixtures (9.2.0-1) ... 253s Setting up python3-iniconfig (1.1.1-2) ... 253s Setting up python3-pandas-lib:armhf (2.3.3+dfsg-1ubuntu1) ... 253s Setting up python3-testfixtures (9.2.0-1) ... 254s Setting up python3-pytz (2025.2-4) ... 254s Setting up python3-packaging (25.0-1) ... 254s Setting up python3-pluggy (1.6.0-1) ... 254s Setting up python3-dateutil (2.9.0-4) ... 254s Setting up python3-pytest (8.3.5-2) ... 255s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 260s Processing triggers for man-db (2.13.1-1) ... 275s autopkgtest [19:33:10]: test command1: pytest-3 275s autopkgtest [19:33:10]: test command1: [----------------------- 277s ============================= test session starts ============================== 277s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 277s rootdir: /tmp/autopkgtest.S0bikQ/build.KCo/src 277s configfile: pytest.ini 277s plugins: typeguard-4.4.2 277s 277s ----------------------------- live log collection ------------------------------ 277s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.S0bikQ/build.KCo/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 277s @pytest.mark.long_test 277s 278s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 278s collected 316 items 278s 278s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 0%] 278s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 0%] 278s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 0%] 278s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] 278s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 1%] 278s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 1%] 278s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 2%] 278s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 2%] 278s tests/core_test.py::test_basic_cif[4UN3] SKIPPED (not running tests ...) [ 2%] 278s tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) [ 3%] 278s tests/core_test.py::test_basic_cif[1K1I] SKIPPED (not running tests ...) [ 3%] 278s tests/core_test.py::test_basic_cif[1NAJ] SKIPPED (not running tests ...) [ 3%] 278s tests/core_test.py::test_basic_cif[1AQO] SKIPPED (not running tests ...) [ 4%] 278s tests/core_test.py::test_basic_cif[7BNA] SKIPPED (not running tests ...) [ 4%] 278s tests/core_test.py::test_basic_cif[5D8V] SKIPPED (not running tests ...) [ 4%] 278s tests/core_test.py::test_basic_cif[4E8M] SKIPPED (not running tests ...) [ 5%] 278s tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 5%] 278s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 5%] 278s tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 6%] 278s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 6%] 278s tests/core_test.py::test_long_pdb[4OSN] SKIPPED (not running tests r...) [ 6%] 278s tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 6%] 278s tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 7%] 278s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 7%] 278s tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 7%] 278s tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 8%] 278s tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 8%] 278s tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 8%] 278s tests/core_test.py::test_long_pdb[2GUS] SKIPPED (not running tests r...) [ 9%] 278s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 9%] 278s tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 9%] 278s tests/core_test.py::test_long_pdb[3NX6] SKIPPED (not running tests r...) [ 10%] 278s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 10%] 278s tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 10%] 278s tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 11%] 278s tests/core_test.py::test_long_pdb[2JIC] SKIPPED (not running tests r...) [ 11%] 278s tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 11%] 278s tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 12%] 278s tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 12%] 278s tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 12%] 278s tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 12%] 278s tests/core_test.py::test_long_pdb[4YKD] SKIPPED (not running tests r...) [ 13%] 278s tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 13%] 278s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 13%] 278s tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 14%] 278s tests/core_test.py::test_long_pdb[2PCY] SKIPPED (not running tests r...) [ 14%] 278s tests/core_test.py::test_long_pdb[1YIB] SKIPPED (not running tests r...) [ 14%] 278s tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 15%] 278s tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 15%] 278s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 15%] 278s tests/core_test.py::test_long_pdb[1R5Q] SKIPPED (not running tests r...) [ 16%] 278s tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 16%] 278s tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 16%] 278s tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 17%] 278s tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 17%] 278s tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 17%] 278s tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 18%] 278s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 18%] 278s tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 18%] 278s tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 18%] 278s tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 19%] 278s tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 19%] 278s tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 19%] 278s tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 20%] 278s tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 20%] 278s tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 20%] 278s tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 21%] 278s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 21%] 278s tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 21%] 278s tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 22%] 278s tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 22%] 278s tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 22%] 278s tests/core_test.py::test_long_pdb[1OX3] SKIPPED (not running tests r...) [ 23%] 278s tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 23%] 278s tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 23%] 278s tests/core_test.py::test_long_pdb[1TVQ] SKIPPED (not running tests r...) [ 24%] 278s tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 24%] 278s tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 24%] 278s tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 25%] 278s tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 25%] 278s tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [ 25%] 278s tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 25%] 278s tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 26%] 278s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 26%] 278s tests/core_test.py::test_long_pdb[4N6T] SKIPPED (not running tests r...) [ 26%] 278s tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 27%] 278s tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 27%] 278s tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 27%] 278s tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 28%] 278s tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 28%] 278s tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 28%] 278s tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 29%] 278s tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 29%] 278s tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 29%] 278s tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 30%] 278s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 30%] 278s tests/core_test.py::test_long_pdb[3C97] SKIPPED (not running tests r...) [ 30%] 278s tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 31%] 278s tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 31%] 278s tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 31%] 278s tests/core_test.py::test_long_pdb[2BYG] SKIPPED (not running tests r...) [ 31%] 278s tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 32%] 278s tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 32%] 278s tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 32%] 278s tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 33%] 278s tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 33%] 278s tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 33%] 278s tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 34%] 278s tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 34%] 278s tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 34%] 278s tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 35%] 278s tests/core_test.py::test_long_pdb[1RIS] SKIPPED (not running tests r...) [ 35%] 278s tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 35%] 278s tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 36%] 278s tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 36%] 278s tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 36%] 278s tests/core_test.py::test_long_pdb[4GQM] SKIPPED (not running tests r...) [ 37%] 278s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 37%] 278s tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 37%] 278s tests/core_test.py::test_long_pdb[4CFI] SKIPPED (not running tests r...) [ 37%] 278s tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 38%] 278s tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 38%] 278s tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 38%] 278s tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 39%] 278s tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 39%] 278s tests/core_test.py::test_long_pdb[2QBV] SKIPPED (not running tests r...) [ 39%] 278s tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 40%] 278s tests/core_test.py::test_long_pdb[2NWD] SKIPPED (not running tests r...) [ 40%] 278s tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 40%] 278s tests/core_test.py::test_long_pdb[2TGI] SKIPPED (not running tests r...) [ 41%] 278s tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [ 41%] 278s tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 41%] 278s tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 42%] 278s tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 42%] 278s tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 42%] 278s tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 43%] 278s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 43%] 278s tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 43%] 278s tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 43%] 278s tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 44%] 278s tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 44%] 278s tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 44%] 278s tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 45%] 278s tests/core_test.py::test_long_pdb[3I35] SKIPPED (not running tests r...) [ 45%] 278s tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 45%] 278s tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 46%] 278s tests/core_test.py::test_long_pdb[1L2P] SKIPPED (not running tests r...) [ 46%] 278s tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 46%] 278s tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 47%] 278s tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 47%] 278s tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 47%] 278s tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 48%] 278s tests/core_test.py::test_long_pdb[1V2Z] SKIPPED (not running tests r...) [ 48%] 278s tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [ 48%] 278s tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 49%] 278s tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 49%] 278s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 49%] 278s tests/core_test.py::test_long_pdb[1PHT] SKIPPED (not running tests r...) [ 50%] 278s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 50%] 278s tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 50%] 278s tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 50%] 278s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 51%] 278s tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 51%] 278s tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 51%] 278s tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 52%] 278s tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 52%] 278s tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 52%] 278s tests/core_test.py::test_long_pdb[2CMP] SKIPPED (not running tests r...) [ 53%] 278s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 53%] 278s tests/core_test.py::test_long_pdb[3QC7] SKIPPED (not running tests r...) [ 53%] 278s tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 54%] 278s tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 54%] 278s tests/core_test.py::test_long_pdb[2J9V] SKIPPED (not running tests r...) [ 54%] 278s tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 55%] 278s tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 55%] 278s tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 55%] 278s tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 56%] 278s tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 56%] 278s tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 56%] 278s tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 56%] 278s tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 57%] 278s tests/core_test.py::test_long_pdb[1P9I] SKIPPED (not running tests r...) [ 57%] 278s tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 57%] 278s tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 58%] 278s tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 58%] 278s tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 58%] 278s tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 59%] 278s tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 59%] 278s tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 59%] 278s tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 60%] 278s tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 60%] 278s tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 60%] 278s tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 61%] 278s tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 61%] 278s tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 61%] 278s tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 62%] 278s tests/core_test.py::test_long_pdb[2NYC] SKIPPED (not running tests r...) [ 62%] 278s tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 62%] 278s tests/core_test.py::test_long_pdb[3WFV] SKIPPED (not running tests r...) [ 62%] 278s tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 63%] 278s tests/core_test.py::test_long_pdb[3T8R] SKIPPED (not running tests r...) [ 63%] 278s tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 63%] 278s tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 64%] 278s tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 64%] 278s tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 64%] 278s tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 65%] 278s tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 65%] 278s tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 65%] 278s tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 66%] 278s tests/core_test.py::test_broken_backbone[2V75] 278s -------------------------------- live log call --------------------------------- 278s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 278s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 278s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 278s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 278s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 278s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 278s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 279s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 279s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 279s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 279s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 279s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 279s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 279s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 279s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 279s CRITICAL PDB2PQR3.6.1:main.py:800 Too few atoms present to reconstruct or cap residue ASN A 95 in structure! This error is generally caused by missing backbone atoms in this biomolecule; you must use an external program to complete gaps in the biomolecule backbone. Heavy atoms missing from ASN A 95: C O CB CG OD1 ND2 OXT CA 279s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 279s XFAIL [ 66%] 279s tests/core_test.py::test_broken_backbone[4MGP] 279s -------------------------------- live log call --------------------------------- 279s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 279s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 279s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 279s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 279s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 279s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 279s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 280s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 280s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 280s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 280s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 280s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 280s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 280s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 280s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 280s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 280s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 280s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 280s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 280s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 280s CRITICAL PDB2PQR3.6.1:main.py:800 Too few atoms present to reconstruct or cap residue SER A 23 in structure! This error is generally caused by missing backbone atoms in this biomolecule; you must use an external program to complete gaps in the biomolecule backbone. Heavy atoms missing from SER A 23: C O CB OG OXT CA 280s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 280s XFAIL [ 66%] 280s tests/core_test.py::test_broken_backbone[3U7T] 280s -------------------------------- live log call --------------------------------- 280s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 280s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 280s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 280s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 280s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 280s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 280s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 281s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 281s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 281s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 281s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 281s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 281s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 281s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 281s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 281s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 281s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 281s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 281s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 313 OG PRO 22 -13.108 -5.696 -15.739 0.0000 0.0000 281s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 281s XFAIL [ 67%] 281s tests/core_test.py::test_broken_backbone[1EJG] 281s -------------------------------- live log call --------------------------------- 281s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 281s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 281s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 281s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 281s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 281s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 281s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 282s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 282s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 282s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 282s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 282s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 282s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 282s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 282s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 282s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 282s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 282s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 282s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 405 CG SER 22 4.661 14.854 -4.058 0.0000 0.0000 282s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 282s XFAIL [ 67%] 282s tests/core_test.py::test_protonated_terminals[C-terminal HID] 282s -------------------------------- live log call --------------------------------- 282s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 282s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 282s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 282s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 282s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 282s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 282s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 282s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 282s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 282s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 282s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 282s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 282s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 282s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 282s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 282s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 282s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 282s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 282s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 282s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 282s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 282s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 282s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 282s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 282s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 282s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 282s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 282s INFO common:common.py:198 0 atoms have position differences > 0 282s INFO common:common.py:198 0 atoms have position differences > 0.01 282s INFO common:common.py:198 0 atoms have charge differences > 0 282s INFO common:common.py:198 0 atoms have charge differences > 0.01 282s INFO common:common.py:198 0 atoms have radius differences > 0 282s INFO common:common.py:198 0 atoms have radius differences > 0.01 282s PASSED [ 67%] 282s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 282s -------------------------------- live log call --------------------------------- 282s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 282s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 282s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 282s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 282s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 282s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 282s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 282s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 282s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 282s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 282s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 282s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 282s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 282s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 282s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 282s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 282s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 282s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 282s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 282s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 282s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 282s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 282s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 282s INFO common:common.py:198 0 atoms have position differences > 0 282s INFO common:common.py:198 0 atoms have position differences > 0.01 282s INFO common:common.py:198 0 atoms have charge differences > 0 282s INFO common:common.py:198 0 atoms have charge differences > 0.01 282s INFO common:common.py:198 0 atoms have radius differences > 0 282s INFO common:common.py:198 0 atoms have radius differences > 0.01 282s PASSED [ 68%] 282s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 282s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 68%] 282s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 282s tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 69%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 69%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 282s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] 283s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] 283s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 72%] 283s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 72%] 283s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 73%] 283s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 73%] 283s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 283s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%] 283s tests/io_test.py::test_read_qcd PASSED [ 74%] 283s tests/io_test.py::test_dx2cube 283s -------------------------------- live log call --------------------------------- 283s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 283s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 283s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 284s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 284s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 285s INFO io_test:io_test.py:68 No differences found in output 285s PASSED [ 74%] 285s tests/ligand_test.py::test_peoe_charges 285s -------------------------------- live log call --------------------------------- 285s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 285s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 285s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 285s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 285s PASSED [ 75%] 286s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 286s -------------------------------- live log call --------------------------------- 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 286s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 286s PASSED [ 75%] 287s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 287s -------------------------------- live log call --------------------------------- 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 287s PASSED [ 75%] 287s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 287s -------------------------------- live log call --------------------------------- 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 287s PASSED [ 75%] 287s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 287s PASSED [ 76%] 287s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 287s PASSED [ 76%] 287s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 287s -------------------------------- live log call --------------------------------- 287s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 287s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 287s PASSED [ 76%] 287s tests/ligand_test.py::test_assign_parameters[adp.mol2] 287s -------------------------------- live log call --------------------------------- 287s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 287s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 287s PASSED [ 77%] 287s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 287s PASSED [ 77%] 287s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 287s PASSED [ 77%] 287s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 287s PASSED [ 78%] 287s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 287s PASSED [ 78%] 287s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 287s PASSED [ 78%] 287s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 287s PASSED [ 79%] 287s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 287s -------------------------------- live log call --------------------------------- 287s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 287s PASSED [ 79%] 287s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 287s -------------------------------- live log call --------------------------------- 287s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 287s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 287s PASSED [ 79%] 287s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 287s -------------------------------- live log call --------------------------------- 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 287s PASSED [ 80%] 288s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 288s -------------------------------- live log call --------------------------------- 288s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 288s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 288s PASSED [ 80%] 288s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 288s -------------------------------- live log call --------------------------------- 288s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 288s PASSED [ 80%] 288s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 288s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 288s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 288s -------------------------------- live log call --------------------------------- 288s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 288s PASSED [ 81%] 288s tests/ligand_test.py::test_formal_charge[adp.mol2] 288s -------------------------------- live log call --------------------------------- 288s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 288s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 288s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 288s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 288s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 288s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 288s PASSED [ 81%] 288s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 288s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 288s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 288s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 288s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 288s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 288s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 288s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 288s -------------------------------- live log call --------------------------------- 288s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 288s PASSED [ 84%] 288s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 288s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 288s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 288s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 288s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 288s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 289s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 290s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 290s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 290s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 290s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 290s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 290s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 290s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 290s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 290s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 290s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 290s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 290s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 290s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 290s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 290s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 290s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 290s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 290s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 290s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 290s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 290s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 290s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 290s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 290s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 290s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 290s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 290s tests/regression_test.py::test_basic[1AFS basic local] 290s -------------------------------- live log call --------------------------------- 290s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 290s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 290s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 290s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 290s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 290s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 290s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 290s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 290s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 290s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 290s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 290s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 290s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 290s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 290s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 290s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 290s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 290s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 290s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 290s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 290s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 290s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 290s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 290s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 290s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 290s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 290s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 290s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 291s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 292s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 292s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 292s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 294s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 294s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 294s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 294s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 294s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 295s WARNING common:common.py:186 6 atoms have position differences > 0 295s INFO common:common.py:198 0 atoms have position differences > 0.01 295s INFO common:common.py:198 0 atoms have charge differences > 0 295s INFO common:common.py:198 0 atoms have charge differences > 0.01 295s INFO common:common.py:198 0 atoms have radius differences > 0 295s INFO common:common.py:198 0 atoms have radius differences > 0.01 295s PASSED [ 95%] 295s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 295s -------------------------------- live log call --------------------------------- 295s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 295s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 295s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 295s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 295s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 295s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 295s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 295s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 295s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 295s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 295s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 295s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 295s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 295s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 295s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 295s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 295s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 295s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 295s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 295s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 295s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 295s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 295s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 295s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 295s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 295s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 295s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 295s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 295s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 296s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 299s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 299s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 299s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 299s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 299s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 299s WARNING common:common.py:186 6 atoms have position differences > 0 299s INFO common:common.py:198 0 atoms have position differences > 0.01 299s INFO common:common.py:198 0 atoms have charge differences > 0 299s INFO common:common.py:198 0 atoms have charge differences > 0.01 299s INFO common:common.py:198 0 atoms have radius differences > 0 299s INFO common:common.py:198 0 atoms have radius differences > 0.01 299s PASSED [ 95%] 299s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 299s -------------------------------- live log call --------------------------------- 299s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 299s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 299s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 299s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 299s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 299s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 299s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 299s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 299s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 299s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 299s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 299s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 299s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 299s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 299s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 299s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 299s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 299s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 299s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 299s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 299s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 299s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 299s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 299s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 300s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 300s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 301s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 304s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 304s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 304s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 304s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 304s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 304s WARNING common:common.py:186 5 atoms have position differences > 0 304s INFO common:common.py:198 0 atoms have position differences > 0.01 304s INFO common:common.py:198 0 atoms have charge differences > 0 304s INFO common:common.py:198 0 atoms have charge differences > 0.01 304s INFO common:common.py:198 0 atoms have radius differences > 0 304s INFO common:common.py:198 0 atoms have radius differences > 0.01 304s PASSED [ 95%] 304s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 304s -------------------------------- live log call --------------------------------- 304s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 304s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 304s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 304s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 304s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 304s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 304s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 304s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 304s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 304s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 304s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 304s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 304s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 304s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 304s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 304s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 304s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 304s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 304s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 304s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 304s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 304s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 304s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 305s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 305s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 306s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 309s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 309s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 309s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 309s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 309s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 309s WARNING common:common.py:186 6 atoms have position differences > 0 309s INFO common:common.py:198 0 atoms have position differences > 0.01 309s INFO common:common.py:198 0 atoms have charge differences > 0 309s INFO common:common.py:198 0 atoms have charge differences > 0.01 309s INFO common:common.py:198 0 atoms have radius differences > 0 309s INFO common:common.py:198 0 atoms have radius differences > 0.01 309s PASSED [ 96%] 309s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 309s -------------------------------- live log call --------------------------------- 309s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 309s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 309s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 309s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 309s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 309s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 309s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 309s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 309s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 309s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 309s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 309s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 309s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 309s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 309s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 309s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 309s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 309s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 309s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 309s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 309s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 309s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 309s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 309s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 310s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 311s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 313s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 313s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 313s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 314s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 314s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 314s WARNING common:common.py:186 6 atoms have position differences > 0 314s INFO common:common.py:198 0 atoms have position differences > 0.01 314s INFO common:common.py:198 0 atoms have charge differences > 0 314s INFO common:common.py:198 0 atoms have charge differences > 0.01 314s INFO common:common.py:198 0 atoms have radius differences > 0 314s INFO common:common.py:198 0 atoms have radius differences > 0.01 314s PASSED [ 96%] 314s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 314s -------------------------------- live log call --------------------------------- 314s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 314s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 314s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 314s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 314s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 314s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 314s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 314s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 314s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 314s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 314s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 314s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 314s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 314s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 314s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 314s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 314s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 314s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 314s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 314s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 314s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 314s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 314s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 314s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 315s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 316s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 318s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 318s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 318s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 319s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 319s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 319s WARNING common:common.py:186 6 atoms have position differences > 0 319s INFO common:common.py:198 0 atoms have position differences > 0.01 319s INFO common:common.py:198 0 atoms have charge differences > 0 319s INFO common:common.py:198 0 atoms have charge differences > 0.01 319s INFO common:common.py:198 0 atoms have radius differences > 0 319s INFO common:common.py:198 0 atoms have radius differences > 0.01 319s PASSED [ 96%] 319s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 319s -------------------------------- live log call --------------------------------- 319s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 319s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 319s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 319s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 319s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 319s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 319s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 319s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 319s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 319s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 319s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 319s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 319s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 319s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 319s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 319s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 319s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 319s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 319s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 319s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 319s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 319s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 319s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 319s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 320s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 320s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 323s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 323s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 323s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 323s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 323s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 324s WARNING common:common.py:186 6 atoms have position differences > 0 324s INFO common:common.py:198 0 atoms have position differences > 0.01 324s INFO common:common.py:198 0 atoms have charge differences > 0 324s INFO common:common.py:198 0 atoms have charge differences > 0.01 324s INFO common:common.py:198 0 atoms have radius differences > 0 324s INFO common:common.py:198 0 atoms have radius differences > 0.01 324s PASSED [ 97%] 324s tests/regression_test.py::test_other_options[1AFS whitespace clean] 324s -------------------------------- live log call --------------------------------- 324s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 324s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 324s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 324s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 324s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 324s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 324s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 324s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 324s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 324s INFO common:common.py:198 0 atoms have position differences > 0 324s INFO common:common.py:198 0 atoms have position differences > 0.01 324s INFO common:common.py:198 0 atoms have charge differences > 0 324s INFO common:common.py:198 0 atoms have charge differences > 0.01 324s INFO common:common.py:198 0 atoms have radius differences > 0 324s INFO common:common.py:198 0 atoms have radius differences > 0.01 324s PASSED [ 97%] 324s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 324s -------------------------------- live log call --------------------------------- 324s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 324s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 324s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 324s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 324s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 324s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 324s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 324s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 324s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 324s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 324s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 324s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 324s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 324s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 324s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 324s INFO common:common.py:198 0 atoms have position differences > 0 324s INFO common:common.py:198 0 atoms have position differences > 0.01 324s INFO common:common.py:198 0 atoms have charge differences > 0 324s INFO common:common.py:198 0 atoms have charge differences > 0.01 324s INFO common:common.py:198 0 atoms have radius differences > 0 324s INFO common:common.py:198 0 atoms have radius differences > 0.01 324s PASSED [ 97%] 324s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 324s -------------------------------- live log call --------------------------------- 324s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 324s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 324s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 324s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 324s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 324s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 324s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 324s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 324s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 324s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 324s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 324s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 324s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 324s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 324s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 324s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 324s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 324s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 324s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 324s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 324s INFO common:common.py:198 0 atoms have position differences > 0 324s INFO common:common.py:198 0 atoms have position differences > 0.01 324s INFO common:common.py:198 0 atoms have charge differences > 0 324s INFO common:common.py:198 0 atoms have charge differences > 0.01 324s INFO common:common.py:198 0 atoms have radius differences > 0 324s INFO common:common.py:198 0 atoms have radius differences > 0.01 324s PASSED [ 98%] 324s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 324s -------------------------------- live log call --------------------------------- 324s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 324s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 324s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 324s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 324s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 324s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 324s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 324s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 324s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 324s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 324s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 324s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 324s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 324s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 324s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 324s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 324s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 324s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 324s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 324s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 324s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 324s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 325s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 325s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 326s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 329s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 329s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 329s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 329s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 329s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 329s WARNING common:common.py:186 6 atoms have position differences > 0 329s INFO common:common.py:198 0 atoms have position differences > 0.01 329s INFO common:common.py:198 0 atoms have charge differences > 0 329s INFO common:common.py:198 0 atoms have charge differences > 0.01 329s INFO common:common.py:198 0 atoms have radius differences > 0 329s INFO common:common.py:198 0 atoms have radius differences > 0.01 329s PASSED [ 98%] 329s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 329s -------------------------------- live log call --------------------------------- 329s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 329s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 329s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 329s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 329s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 329s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 329s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 329s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 329s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 329s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 329s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 329s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 329s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 329s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 329s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 329s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 329s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 329s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 329s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 329s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 329s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 329s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 329s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 329s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 330s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 331s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 333s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 333s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 333s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 334s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 334s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 334s WARNING common:common.py:186 6 atoms have position differences > 0 334s INFO common:common.py:198 0 atoms have position differences > 0.01 334s INFO common:common.py:198 0 atoms have charge differences > 0 334s INFO common:common.py:198 0 atoms have charge differences > 0.01 334s INFO common:common.py:198 0 atoms have radius differences > 0 334s INFO common:common.py:198 0 atoms have radius differences > 0.01 334s PASSED [ 98%] 334s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 334s -------------------------------- live log call --------------------------------- 334s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 334s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 334s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 334s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 334s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 334s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 334s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 334s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 334s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 334s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 334s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 334s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 334s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 334s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 334s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 334s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 334s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 334s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 334s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 334s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 334s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 334s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 334s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 334s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 334s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 335s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 335s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 337s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 337s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 337s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 337s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 337s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 337s WARNING common:common.py:186 6 atoms have position differences > 0 337s INFO common:common.py:198 0 atoms have position differences > 0.01 337s INFO common:common.py:198 0 atoms have charge differences > 0 337s INFO common:common.py:198 0 atoms have charge differences > 0.01 337s INFO common:common.py:198 0 atoms have radius differences > 0 337s INFO common:common.py:198 0 atoms have radius differences > 0.01 337s PASSED [ 99%] 337s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 337s -------------------------------- live log call --------------------------------- 337s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 337s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 337s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 337s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 337s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 337s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 337s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 337s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 338s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 338s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 338s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 338s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 338s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 338s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 338s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 338s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 338s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 338s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 338s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 338s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 338s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 338s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 338s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 338s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 338s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 339s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 342s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 342s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 342s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 342s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 342s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 342s WARNING common:common.py:186 6 atoms have position differences > 0 342s INFO common:common.py:198 0 atoms have position differences > 0.01 342s INFO common:common.py:198 0 atoms have charge differences > 0 342s INFO common:common.py:198 0 atoms have charge differences > 0.01 342s INFO common:common.py:198 0 atoms have radius differences > 0 342s INFO common:common.py:198 0 atoms have radius differences > 0.01 342s PASSED [ 99%] 342s tests/test_version.py::test_version_exists PASSED [ 99%] 342s tests/test_version.py::test_version PASSED [100%] 342s 342s ============ 92 passed, 220 skipped, 4 xfailed in 65.38s (0:01:05) ============= 343s autopkgtest [19:34:18]: test command1: -----------------------] 347s command1 PASS 347s autopkgtest [19:34:22]: test command1: - - - - - - - - - - results - - - - - - - - - - 351s autopkgtest [19:34:26]: @@@@@@@@@@@@@@@@@@@@ summary 351s installation-test PASS 351s pdb2pka-test PASS 351s command1 PASS