0s autopkgtest [12:02:31]: starting date and time: 2025-02-19 12:02:31+0000 0s autopkgtest [12:02:31]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:02:31]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p39f34ta/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:sphinx --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- lxd -r lxd-armhf-10.145.243.188 lxd-armhf-10.145.243.188:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [12:03:23]: testbed dpkg architecture: armhf 55s autopkgtest [12:03:26]: testbed apt version: 2.9.14ubuntu1 59s autopkgtest [12:03:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [12:03:32]: testbed release detected to be: None 70s autopkgtest [12:03:41]: updating testbed package index (apt update) 73s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [249 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [110 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [110 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [99.0 kB] 73s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Components [4980 B] 73s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [760 B] 73s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Components [216 B] 73s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [636 kB] 73s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Components [292 kB] 73s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3116 B] 73s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Components [1072 B] 73s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 74s Get:18 http://ftpmaster.internal/ubuntu plucky/main Sources [1382 kB] 74s Get:19 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 74s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted Sources [16.3 kB] 74s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1369 kB] 74s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf Components [401 kB] 74s Get:23 http://ftpmaster.internal/ubuntu plucky/restricted armhf Packages [2900 B] 74s Get:24 http://ftpmaster.internal/ubuntu plucky/restricted armhf Components [196 B] 74s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 74s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf Components [3939 kB] 74s Get:27 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [173 kB] 74s Get:28 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Components [39.8 kB] 74s Get:29 http://ftpmaster.internal/ubuntu plucky-updates/main armhf Components [208 B] 74s Get:30 http://ftpmaster.internal/ubuntu plucky-updates/restricted armhf Components [212 B] 74s Get:31 http://ftpmaster.internal/ubuntu plucky-updates/universe armhf Components [212 B] 74s Get:32 http://ftpmaster.internal/ubuntu plucky-updates/multiverse armhf Components [212 B] 74s Get:33 http://ftpmaster.internal/ubuntu plucky-security/main armhf Components [204 B] 74s Get:34 http://ftpmaster.internal/ubuntu plucky-security/restricted armhf Components [212 B] 74s Get:35 http://ftpmaster.internal/ubuntu plucky-security/universe armhf Components [208 B] 75s Get:36 http://ftpmaster.internal/ubuntu plucky-security/multiverse armhf Components [212 B] 81s Fetched 46.2 MB in 6s (7249 kB/s) 82s Reading package lists... 89s autopkgtest [12:04:00]: upgrading testbed (apt dist-upgrade and autopurge) 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 92s Starting 2 pkgProblemResolver with broken count: 0 92s Done 93s Entering ResolveByKeep 93s 93s The following packages were automatically installed and are no longer required: 93s libassuan0 libicu74 libnsl2 libpython3.12-minimal libpython3.12-stdlib 93s libunwind8 linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic python3.12 93s python3.12-minimal 93s Use 'apt autoremove' to remove them. 94s The following NEW packages will be installed: 94s gcc-15-base libapt-pkg7.0 libicu76 libpython3.13-minimal 94s libpython3.13-stdlib linux-headers-6.12.0-15 linux-headers-6.12.0-15-generic 94s login.defs openssl-provider-legacy python3-bcrypt python3.13 94s python3.13-minimal 94s The following packages will be upgraded: 94s apparmor apport apport-core-dump-handler appstream apt apt-utils base-passwd 94s bash bash-completion bind9-dnsutils bind9-host bind9-libs binutils 94s binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils 94s btrfs-progs busybox-initramfs busybox-static ca-certificates cloud-init 94s cloud-init-base console-setup console-setup-linux coreutils cron 94s cron-daemon-common curl dash dbus dbus-bin dbus-daemon 94s dbus-session-bus-common dbus-system-bus-common dbus-user-session dhcpcd-base 94s diffutils dirmngr distro-info dmsetup dpkg dpkg-dev dracut-install e2fsprogs 94s e2fsprogs-l10n ed eject ethtool fdisk fwupd gcc-14-base gettext-base 94s gir1.2-girepository-2.0 gir1.2-glib-2.0 gir1.2-packagekitglib-1.0 gnupg 94s gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpgconf gpgsm gpgv 94s groff-base gzip htop ibverbs-providers init init-system-helpers 94s initramfs-tools initramfs-tools-bin initramfs-tools-core iproute2 iptables 94s iputils-ping iputils-tracepath keyboard-configuration keyboxd kpartx 94s krb5-locales libapparmor1 libappstream5 libapt-pkg6.0t64 libarchive13t64 94s libatomic1 libbinutils libblkid1 libblockdev-crypto3 libblockdev-fs3 94s libblockdev-loop3 libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 94s libblockdev-swap3 libblockdev-utils3 libblockdev3 libbpf1 libc-bin libc6 94s libcap-ng0 libcom-err2 libcrypt1 libctf-nobfd0 libctf0 libcurl3t64-gnutls 94s libcurl4t64 libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl 94s libedit2 libext2fs2t64 libfdisk1 libffi8 libfribidi0 libftdi1-2 libfwupd3 94s libgcc-s1 libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-bin 94s libglib2.0-data libgnutls30t64 libgpg-error-l10n libgpg-error0 libgpgme11t64 94s libgssapi-krb5-2 libgstreamer1.0-0 libgudev-1.0-0 libhogweed6t64 libibverbs1 94s libicu74 libip4tc2 libip6tc2 libjson-glib-1.0-0 libjson-glib-1.0-common 94s libk5crypto3 libkrb5-3 libkrb5support0 libldap-common libldap2 liblsof0 94s liblz4-1 libmaxminddb0 libmount1 libncurses6 libncursesw6 libnetplan1 94s libnettle8t64 libnewt0.52 libnftables1 libnftnl11 libnpth0t64 libnspr4 94s libnss-systemd libnss3 libnvme1t64 libp11-kit0 libpackagekit-glib2-18 94s libpam-systemd libpcap0.8t64 libpng16-16t64 libpolkit-agent-1-0 94s libpolkit-gobject-1-0 libprotobuf-c1 libpython3-stdlib libpython3.12-minimal 94s libpython3.12-stdlib libqmi-glib5 libqmi-proxy libreadline8t64 libsasl2-2 94s libsasl2-modules libsasl2-modules-db libselinux1 libsemanage-common 94s libsemanage2 libsframe1 libsmartcols1 libss2 libssl3t64 libstdc++6 94s libsystemd-shared libsystemd0 libtasn1-6 libtinfo6 libtraceevent1 94s libtraceevent1-plugin libudev1 libudisks2-0 libunistring5 liburcu8t64 94s libusb-1.0-0 libuuid1 libvolume-key1 libwrap0 libxdmcp6 libxkbcommon0 94s libxml2 libxtables12 libxxhash0 libyaml-0-2 libzstd1 linux-headers-generic 94s locales login logsave lshw lsof make mawk mount multipath-tools nano 94s ncurses-base ncurses-bin ncurses-term netcat-openbsd netplan-generator 94s netplan.io nftables openssl packagekit packagekit-tools passwd pci.ids 94s pinentry-curses polkitd pollinate powermgmt-base psmisc publicsuffix 94s python-apt-common python-babel-localedata python3 python3-apport python3-apt 94s python3-attr python3-babel python3-certifi python3-chardet 94s python3-cryptography python3-distro-info python3-gdbm python3-gi 94s python3-idna python3-jinja2 python3-json-pointer python3-jsonpatch 94s python3-jsonschema python3-jwt python3-launchpadlib python3-lazr.uri 94s python3-minimal python3-more-itertools python3-netplan python3-newt 94s python3-oauthlib python3-openssl python3-pkg-resources 94s python3-problem-report python3-pygments python3-referencing python3-rich 94s python3-setuptools python3-software-properties python3-urllib3 94s python3-wadllib python3.12 python3.12-gdbm python3.12-minimal 94s python3.13-gdbm readline-common rsync rsyslog software-properties-common 94s systemd systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 94s tar tzdata ubuntu-minimal ubuntu-standard ucf udev udisks2 ufw 94s unattended-upgrades usb.ids util-linux uuid-runtime whiptail xauth xfsprogs 94s zstd 94s 299 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 135 MB of archives. 94s After this operation, 198 MB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf bash armhf 5.2.37-1ubuntu1 [677 kB] 94s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf bsdutils armhf 1:2.40.2-14ubuntu1 [110 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf coreutils armhf 9.5-1ubuntu1 [1275 kB] 94s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf dash armhf 0.5.12-12ubuntu1 [87.4 kB] 94s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf diffutils armhf 1:3.10-2 [172 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-15-base armhf 15-20250213-1ubuntu1 [53.2 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 15-20250213-1ubuntu1 [40.6 kB] 94s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libc6 armhf 2.40-4ubuntu1 [2866 kB] 94s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libxxhash0 armhf 0.8.3-2 [30.8 kB] 94s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf liblz4-1 armhf 1.10.0-3 [57.2 kB] 94s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf openssl-provider-legacy armhf 3.4.0-1ubuntu2 [29.4 kB] 94s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libssl3t64 armhf 3.4.0-1ubuntu2 [1756 kB] 94s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libzstd1 armhf 1.5.6+dfsg-2 [266 kB] 94s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 15-20250213-1ubuntu1 [725 kB] 94s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 257.2-3ubuntu1 [42.1 kB] 94s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-session-bus-common all 1.16.0-1ubuntu1 [53.1 kB] 94s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 257.2-3ubuntu1 [11.9 kB] 94s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 257.2-3ubuntu1 [238 kB] 94s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-user-session armhf 1.16.0-1ubuntu1 [9684 B] 94s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libapparmor1 armhf 4.1.0~beta1-0ubuntu5 [47.3 kB] 94s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-4 [13.8 kB] 94s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libselinux1 armhf 3.7-3ubuntu2 [73.2 kB] 95s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-system-bus-common all 1.16.0-1ubuntu1 [54.3 kB] 95s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-bin armhf 1.16.0-1ubuntu1 [37.9 kB] 95s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf dbus armhf 1.16.0-1ubuntu1 [28.1 kB] 95s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf dbus-daemon armhf 1.16.0-1ubuntu1 [111 kB] 95s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libdbus-1-3 armhf 1.16.0-1ubuntu1 [162 kB] 95s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 257.2-3ubuntu1 [315 kB] 95s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 257.2-3ubuntu1 [126 kB] 95s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses6 armhf 6.5+20250125-2 [88.8 kB] 95s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libncursesw6 armhf 6.5+20250125-2 [118 kB] 95s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libtinfo6 armhf 6.5+20250125-2 [91.9 kB] 95s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf bsdextrautils armhf 2.40.2-14ubuntu1 [94.2 kB] 95s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf eject armhf 2.40.2-14ubuntu1 [63.4 kB] 95s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf fdisk armhf 2.40.2-14ubuntu1 [157 kB] 95s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblkid1 armhf 2.40.2-14ubuntu1 [169 kB] 95s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libmount1 armhf 2.40.2-14ubuntu1 [194 kB] 95s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libsmartcols1 armhf 2.40.2-14ubuntu1 [137 kB] 95s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libuuid1 armhf 2.40.2-14ubuntu1 [41.0 kB] 95s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf util-linux armhf 2.40.2-14ubuntu1 [1190 kB] 95s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf uuid-runtime armhf 2.40.2-14ubuntu1 [63.7 kB] 95s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libfdisk1 armhf 2.40.2-14ubuntu1 [217 kB] 95s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf mount armhf 2.40.2-14ubuntu1 [158 kB] 95s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf readline-common all 8.2-6 [56.5 kB] 95s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline8t64 armhf 8.2-6 [131 kB] 95s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt1 armhf 1:4.4.38-1 [91.7 kB] 95s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 257.2-3ubuntu1 [2203 kB] 95s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 257.2-3ubuntu1 [3028 kB] 95s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 257.2-3ubuntu1 [1402 kB] 95s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 257.2-3ubuntu1 [164 kB] 95s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 257.2-3ubuntu1 [193 kB] 95s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 257.2-3ubuntu1 [494 kB] 95s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libapt-pkg6.0t64 armhf 2.9.29 [1086 kB] 95s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf tar armhf 1.35+dfsg-3.1 [240 kB] 95s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg armhf 1.22.11ubuntu4 [1242 kB] 95s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf gzip armhf 1.13-1ubuntu2 [98.1 kB] 95s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf ncurses-bin armhf 6.5+20250125-2 [179 kB] 95s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libdebconfclient0 armhf 0.274ubuntu1 [11.2 kB] 95s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.6 [53.4 kB] 95s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf init-system-helpers all 1.68 [39.0 kB] 95s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libc-bin armhf 2.40-4ubuntu1 [542 kB] 95s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf ncurses-base all 6.5+20250125-2 [25.8 kB] 95s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf ncurses-term all 6.5+20250125-2 [276 kB] 95s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libapt-pkg7.0 armhf 2.9.30 [1065 kB] 95s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf apt armhf 2.9.30 [1390 kB] 95s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf apt-utils armhf 2.9.30 [214 kB] 95s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf libgpg-error-l10n all 1.51-3 [8800 B] 95s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libgpg-error0 armhf 1.51-3 [64.8 kB] 95s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libnpth0t64 armhf 1.8-2 [7572 B] 95s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf gpg-wks-client armhf 2.4.4-2ubuntu22 [87.5 kB] 95s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf dirmngr armhf 2.4.4-2ubuntu22 [347 kB] 95s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf gpgsm armhf 2.4.4-2ubuntu22 [242 kB] 95s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg-utils armhf 2.4.4-2ubuntu22 [159 kB] 95s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf gpg-agent armhf 2.4.4-2ubuntu22 [237 kB] 95s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf gpg armhf 2.4.4-2ubuntu22 [525 kB] 95s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf gpgconf armhf 2.4.4-2ubuntu22 [116 kB] 95s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg all 2.4.4-2ubuntu22 [359 kB] 95s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf keyboxd armhf 2.4.4-2ubuntu22 [111 kB] 95s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu2 [40.6 kB] 95s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libnettle8t64 armhf 3.10.1-1 [188 kB] 95s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libhogweed6t64 armhf 3.10.1-1 [188 kB] 95s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libffi8 armhf 3.4.7-1 [21.1 kB] 95s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libp11-kit0 armhf 0.25.5-2ubuntu3 [261 kB] 95s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libtasn1-6 armhf 4.20.0-2 [38.2 kB] 96s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libunistring5 armhf 1.3-1 [583 kB] 96s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.9-2ubuntu1 [961 kB] 96s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8build1 [19.0 kB] 96s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8build1 [49.9 kB] 96s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.9+dfsg-1~exp2ubuntu1 [33.2 kB] 96s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.9+dfsg-1~exp2ubuntu1 [177 kB] 96s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf gpgv armhf 2.4.4-2ubuntu22 [225 kB] 96s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf e2fsprogs-l10n all 1.47.2-1ubuntu1 [7030 B] 96s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf logsave armhf 1.47.2-1ubuntu1 [25.7 kB] 96s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf ubuntu-minimal armhf 1.547 [11.4 kB] 96s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf initramfs-tools all 0.145ubuntu2 [7948 B] 96s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf initramfs-tools-core all 0.145ubuntu2 [51.5 kB] 96s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf libext2fs2t64 armhf 1.47.2-1ubuntu1 [207 kB] 96s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf e2fsprogs armhf 1.47.2-1ubuntu1 [588 kB] 96s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf console-setup-linux all 1.226ubuntu3 [1880 kB] 96s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf console-setup all 1.226ubuntu3 [110 kB] 96s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf keyboard-configuration all 1.226ubuntu3 [212 kB] 96s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf dhcpcd-base armhf 1:10.1.0-7 [188 kB] 96s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf init armhf 1.68 [6296 B] 96s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-2 [158 kB] 96s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf iptables armhf 1.8.11-2ubuntu1 [342 kB] 96s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libip4tc2 armhf 1.8.11-2ubuntu1 [21.7 kB] 96s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libip6tc2 armhf 1.8.11-2ubuntu1 [22.1 kB] 96s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libnftnl11 armhf 1.2.8-1 [53.3 kB] 96s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libxtables12 armhf 1.8.11-2ubuntu1 [33.0 kB] 96s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.13.0-1ubuntu1 [1096 kB] 96s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf iputils-ping armhf 3:20240905-1ubuntu1 [45.0 kB] 96s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf locales all 2.40-4ubuntu1 [4224 kB] 97s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf login.defs all 1:4.16.0-7ubuntu1 [38.5 kB] 97s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf login armhf 1:4.16.0-2+really2.40.2-14ubuntu1 [85.0 kB] 97s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf mawk armhf 1.3.4.20250131-1 [119 kB] 97s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf netcat-openbsd armhf 1.228-1 [42.4 kB] 97s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.2-1 [868 kB] 97s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.2-1 [2012 kB] 97s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cryptography armhf 43.0.0-1 [925 kB] 97s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf python3-minimal armhf 3.13.1-1~exp2 [27.6 kB] 97s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf python3 armhf 3.13.1-1~exp2 [23.9 kB] 97s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf python3-bcrypt armhf 4.2.0-2.1 [239 kB] 97s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2025a-2ubuntu1 [198 kB] 97s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.2-1 [1969 kB] 97s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.2-1 [734 kB] 97s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-stdlib armhf 3.13.1-1~exp2 [10.2 kB] 97s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-girepository-2.0 armhf 1.82.0-4 [25.3 kB] 97s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-glib-2.0 armhf 2.83.3-2 [184 kB] 97s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libgirepository-1.0-1 armhf 1.82.0-4 [109 kB] 97s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-data all 2.83.3-2 [52.7 kB] 97s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-bin armhf 2.83.3-2 [92.7 kB] 97s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 15-20250213-1ubuntu1 [7938 B] 97s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf libglib2.0-0t64 armhf 2.83.3-2 [1452 kB] 97s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf netplan-generator armhf 1.1.2-2ubuntu1 [60.8 kB] 97s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf libyaml-0-2 armhf 0.2.5-2 [45.3 kB] 97s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf python3-netplan armhf 1.1.2-2ubuntu1 [24.2 kB] 97s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf netplan.io armhf 1.1.2-2ubuntu1 [67.7 kB] 97s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf libnetplan1 armhf 1.1.2-2ubuntu1 [123 kB] 97s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf ethtool armhf 1:6.11-1 [222 kB] 97s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf libsemanage-common all 3.7-2.1 [7198 B] 97s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf libsemanage2 armhf 3.7-2.1 [85.4 kB] 97s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf passwd armhf 1:4.16.0-7ubuntu1 [1041 kB] 97s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-4ubuntu1 [20.1 kB] 97s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-4ubuntu1 [39.7 kB] 97s Get:145 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-4ubuntu1 [17.3 kB] 97s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf dracut-install armhf 106-2ubuntu1 [38.7 kB] 97s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf initramfs-tools-bin armhf 0.145ubuntu2 [24.5 kB] 97s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf busybox-initramfs armhf 1:1.37.0-4ubuntu1 [188 kB] 97s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.9-1 [671 kB] 97s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.9-1 [1946 kB] 97s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.9-1 [2012 kB] 97s Get:152 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.9-1 [825 kB] 97s Get:153 http://ftpmaster.internal/ubuntu plucky/main armhf cron armhf 3.0pl1-192ubuntu1 [84.2 kB] 97s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf rsync armhf 3.4.1-0syncable1 [422 kB] 97s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf python-apt-common all 2.9.8 [21.1 kB] 97s Get:156 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apt armhf 2.9.8 [174 kB] 97s Get:157 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-5 [13.6 kB] 97s Get:158 http://ftpmaster.internal/ubuntu plucky/main armhf python3-launchpadlib all 2.1.0-1 [126 kB] 97s Get:159 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.31.0-0ubuntu5 [25.5 kB] 97s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.31.0-0ubuntu5 [93.1 kB] 97s Get:161 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gi armhf 3.50.0-4 [260 kB] 97s Get:162 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.31.0-0ubuntu5 [18.4 kB] 97s Get:163 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.31.0-0ubuntu5 [83.0 kB] 98s Get:164 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-17ubuntu1 [53.5 kB] 98s Get:165 http://ftpmaster.internal/ubuntu plucky/main armhf libcom-err2 armhf 1.47.2-1ubuntu1 [25.6 kB] 98s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf libss2 armhf 1.47.2-1ubuntu1 [15.6 kB] 98s Get:167 http://ftpmaster.internal/ubuntu plucky/main armhf openssl armhf 3.4.0-1ubuntu2 [1159 kB] 98s Get:168 http://ftpmaster.internal/ubuntu plucky/main armhf ca-certificates all 20241223 [165 kB] 98s Get:169 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info armhf 1.13 [19.1 kB] 98s Get:170 http://ftpmaster.internal/ubuntu plucky/main armhf krb5-locales all 1.21.3-4ubuntu1 [14.7 kB] 98s Get:171 http://ftpmaster.internal/ubuntu plucky/main armhf libfribidi0 armhf 1.0.16-1 [24.3 kB] 98s Get:172 http://ftpmaster.internal/ubuntu plucky/main armhf libgssapi-krb5-2 armhf 1.21.3-4ubuntu1 [121 kB] 98s Get:173 http://ftpmaster.internal/ubuntu plucky/main armhf libkrb5-3 armhf 1.21.3-4ubuntu1 [314 kB] 98s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf libkrb5support0 armhf 1.21.3-4ubuntu1 [31.8 kB] 98s Get:175 http://ftpmaster.internal/ubuntu plucky/main armhf libk5crypto3 armhf 1.21.3-4ubuntu1 [78.6 kB] 98s Get:176 http://ftpmaster.internal/ubuntu plucky/main armhf libicu74 armhf 74.2-1ubuntu6 [10.5 MB] 98s Get:177 http://ftpmaster.internal/ubuntu plucky/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2ubuntu3 [599 kB] 98s Get:178 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pygments all 2.18.0+dfsg-2 [835 kB] 98s Get:179 http://ftpmaster.internal/ubuntu plucky/main armhf python3-rich all 13.9.4-1 [190 kB] 98s Get:180 http://ftpmaster.internal/ubuntu plucky/main armhf ucf all 3.0049 [43.3 kB] 98s Get:181 http://ftpmaster.internal/ubuntu plucky/main armhf rsyslog armhf 8.2412.0-2ubuntu1 [471 kB] 98s Get:182 http://ftpmaster.internal/ubuntu plucky/main armhf apparmor armhf 4.1.0~beta1-0ubuntu5 [589 kB] 98s Get:183 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.16.0-7 [214 kB] 98s Get:184 http://ftpmaster.internal/ubuntu plucky/main armhf libmaxminddb0 armhf 1.12.2-1 [16.9 kB] 98s Get:185 http://ftpmaster.internal/ubuntu plucky/main armhf liburcu8t64 armhf 0.15.0-1 [57.3 kB] 98s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf bind9-dnsutils armhf 1:9.20.0-2ubuntu4 [155 kB] 98s Get:187 http://ftpmaster.internal/ubuntu plucky/main armhf bind9-host armhf 1:9.20.0-2ubuntu4 [46.2 kB] 98s Get:188 http://ftpmaster.internal/ubuntu plucky/main armhf bind9-libs armhf 1:9.20.0-2ubuntu4 [1176 kB] 98s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf libedit2 armhf 3.1-20250104-1 [79.3 kB] 98s Get:190 http://ftpmaster.internal/ubuntu plucky/main armhf busybox-static armhf 1:1.37.0-4ubuntu1 [857 kB] 98s Get:191 http://ftpmaster.internal/ubuntu plucky/main armhf cron-daemon-common all 3.0pl1-192ubuntu1 [14.5 kB] 98s Get:192 http://ftpmaster.internal/ubuntu plucky/main armhf libdevmapper1.02.1 armhf 2:1.02.201-1ubuntu1 [137 kB] 98s Get:193 http://ftpmaster.internal/ubuntu plucky/main armhf dmsetup armhf 2:1.02.201-1ubuntu1 [80.4 kB] 98s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf ed armhf 1.21-1 [52.8 kB] 98s Get:195 http://ftpmaster.internal/ubuntu plucky/main armhf gettext-base armhf 0.23.1-1 [43.3 kB] 98s Get:196 http://ftpmaster.internal/ubuntu plucky/main armhf groff-base armhf 1.23.0-7 [949 kB] 98s Get:197 http://ftpmaster.internal/ubuntu plucky/main armhf libibverbs1 armhf 55.0-1ubuntu1 [58.5 kB] 98s Get:198 http://ftpmaster.internal/ubuntu plucky/main armhf ibverbs-providers armhf 55.0-1ubuntu1 [27.6 kB] 98s Get:199 http://ftpmaster.internal/ubuntu plucky/main armhf iputils-tracepath armhf 3:20240905-1ubuntu1 [13.3 kB] 98s Get:200 http://ftpmaster.internal/ubuntu plucky/main armhf nftables armhf 1.1.1-1build1 [70.8 kB] 98s Get:201 http://ftpmaster.internal/ubuntu plucky/main armhf libnftables1 armhf 1.1.1-1build1 [321 kB] 98s Get:202 http://ftpmaster.internal/ubuntu plucky/main armhf libpcap0.8t64 armhf 1.10.5-2ubuntu1 [140 kB] 99s Get:203 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.46-4 [171 kB] 99s Get:204 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.4-2 [19.0 kB] 99s Get:205 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.4-2 [53.8 kB] 99s Get:206 http://ftpmaster.internal/ubuntu plucky/main armhf libusb-1.0-0 armhf 2:1.0.27-2 [49.5 kB] 99s Get:207 http://ftpmaster.internal/ubuntu plucky/main armhf libxdmcp6 armhf 1:1.1.5-1 [9060 B] 99s Get:208 http://ftpmaster.internal/ubuntu plucky/main armhf libxkbcommon0 armhf 1.7.0-2 [113 kB] 99s Get:209 http://ftpmaster.internal/ubuntu plucky/main armhf lshw armhf 02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1 [311 kB] 99s Get:210 http://ftpmaster.internal/ubuntu plucky/main armhf lsof armhf 4.99.4+dfsg-1 [239 kB] 99s Get:211 http://ftpmaster.internal/ubuntu plucky/main armhf liblsof0 armhf 4.99.4+dfsg-1 [60.7 kB] 99s Get:212 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.3-1 [277 kB] 99s Get:213 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2025.02.12-1 [284 kB] 99s Get:214 http://ftpmaster.internal/ubuntu plucky/main armhf powermgmt-base all 1.38 [7378 B] 99s Get:215 http://ftpmaster.internal/ubuntu plucky/main armhf psmisc armhf 23.7-2 [177 kB] 99s Get:216 http://ftpmaster.internal/ubuntu plucky/main armhf publicsuffix all 20250108.1153-0.1 [134 kB] 99s Get:217 http://ftpmaster.internal/ubuntu plucky/main armhf python3-distro-info all 1.13 [7798 B] 99s Get:218 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.2-1 [30.2 kB] 99s Get:219 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.9-1 [29.3 kB] 99s Get:220 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gdbm armhf 3.13.1-1 [8668 B] 99s Get:221 http://ftpmaster.internal/ubuntu plucky/main armhf ubuntu-standard armhf 1.547 [11.4 kB] 99s Get:222 http://ftpmaster.internal/ubuntu plucky/main armhf ufw all 0.36.2-9 [170 kB] 99s Get:223 http://ftpmaster.internal/ubuntu plucky/main armhf usb.ids all 2025.01.14-1 [223 kB] 99s Get:224 http://ftpmaster.internal/ubuntu plucky/main armhf xauth armhf 1:1.1.2-1.1 [23.0 kB] 99s Get:225 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl3t64-gnutls armhf 8.12.0+git20250209.89ed161+ds-1ubuntu1 [330 kB] 99s Get:226 http://ftpmaster.internal/ubuntu plucky/main armhf libappstream5 armhf 1.0.4-1 [211 kB] 99s Get:227 http://ftpmaster.internal/ubuntu plucky/main armhf appstream armhf 1.0.4-1 [67.3 kB] 99s Get:228 http://ftpmaster.internal/ubuntu plucky/main armhf libctf0 armhf 2.44-1ubuntu1 [74.4 kB] 99s Get:229 http://ftpmaster.internal/ubuntu plucky/main armhf libctf-nobfd0 armhf 2.44-1ubuntu1 [77.6 kB] 99s Get:230 http://ftpmaster.internal/ubuntu plucky/main armhf binutils-arm-linux-gnueabihf armhf 2.44-1ubuntu1 [995 kB] 99s Get:231 http://ftpmaster.internal/ubuntu plucky/main armhf libbinutils armhf 2.44-1ubuntu1 [405 kB] 99s Get:232 http://ftpmaster.internal/ubuntu plucky/main armhf binutils armhf 2.44-1ubuntu1 [3238 B] 99s Get:233 http://ftpmaster.internal/ubuntu plucky/main armhf binutils-common armhf 2.44-1ubuntu1 [216 kB] 99s Get:234 http://ftpmaster.internal/ubuntu plucky/main armhf libsframe1 armhf 2.44-1ubuntu1 [12.5 kB] 99s Get:235 http://ftpmaster.internal/ubuntu plucky/main armhf btrfs-progs armhf 6.12-1build1 [884 kB] 99s Get:236 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2 [109 kB] 99s Get:237 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-3 [8444 B] 99s Get:238 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-5 [12.3 kB] 99s Get:239 http://ftpmaster.internal/ubuntu plucky/main armhf python3-attr all 25.1.0-1 [50.4 kB] 99s Get:240 http://ftpmaster.internal/ubuntu plucky/main armhf python3-referencing all 0.35.1-2ubuntu1 [21.9 kB] 100s Get:241 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonschema all 4.19.2-6ubuntu1 [65.5 kB] 100s Get:242 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jwt all 2.10.1-2 [21.0 kB] 100s Get:243 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-3 [89.9 kB] 100s Get:244 http://ftpmaster.internal/ubuntu plucky/main armhf cloud-init-base all 25.1~3geb1965a4-0ubuntu1 [615 kB] 100s Get:245 http://ftpmaster.internal/ubuntu plucky/main armhf curl armhf 8.12.0+git20250209.89ed161+ds-1ubuntu1 [247 kB] 100s Get:246 http://ftpmaster.internal/ubuntu plucky/main armhf libcurl4t64 armhf 8.12.0+git20250209.89ed161+ds-1ubuntu1 [335 kB] 100s Get:247 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg-dev all 1.22.11ubuntu4 [1088 kB] 100s Get:248 http://ftpmaster.internal/ubuntu plucky/main armhf libdpkg-perl all 1.22.11ubuntu4 [279 kB] 100s Get:249 http://ftpmaster.internal/ubuntu plucky/main armhf make armhf 4.4.1-1 [180 kB] 100s Get:250 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive13t64 armhf 3.7.7-0ubuntu1 [335 kB] 100s Get:251 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.6+ds-1 [5636 B] 100s Get:252 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.6+ds-1 [59.5 kB] 100s Get:253 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.5-1 [5151 kB] 100s Get:254 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.5-1 [125 kB] 100s Get:255 http://ftpmaster.internal/ubuntu plucky/main armhf polkitd armhf 126-2 [92.5 kB] 100s Get:256 http://ftpmaster.internal/ubuntu plucky/main armhf libpolkit-agent-1-0 armhf 126-2 [15.1 kB] 100s Get:257 http://ftpmaster.internal/ubuntu plucky/main armhf libpolkit-gobject-1-0 armhf 126-2 [45.0 kB] 100s Get:258 http://ftpmaster.internal/ubuntu plucky/main armhf libprotobuf-c1 armhf 1.5.1-1ubuntu1 [18.1 kB] 100s Get:259 http://ftpmaster.internal/ubuntu plucky/main armhf libqmi-proxy armhf 1.35.6-1 [5878 B] 100s Get:260 http://ftpmaster.internal/ubuntu plucky/main armhf libqmi-glib5 armhf 1.35.6-1 [928 kB] 100s Get:261 http://ftpmaster.internal/ubuntu plucky/main armhf libpackagekit-glib2-18 armhf 1.3.0-3build1 [109 kB] 100s Get:262 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-packagekitglib-1.0 armhf 1.3.0-3build1 [25.5 kB] 100s Get:263 http://ftpmaster.internal/ubuntu plucky/main armhf gnupg-l10n all 2.4.4-2ubuntu22 [66.4 kB] 100s Get:264 http://ftpmaster.internal/ubuntu plucky/main armhf htop armhf 3.3.0-5 [140 kB] 100s Get:265 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.3.0-1 [17.5 kB] 100s Get:266 http://ftpmaster.internal/ubuntu plucky/main armhf libnspr4 armhf 2:4.36-1ubuntu1 [94.5 kB] 100s Get:267 http://ftpmaster.internal/ubuntu plucky/main armhf libnss3 armhf 2:3.107-1ubuntu1 [1315 kB] 100s Get:268 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.24.1-4ubuntu1 [125 kB] 100s Get:269 http://ftpmaster.internal/ubuntu plucky/main armhf libvolume-key1 armhf 0.3.12-9 [39.1 kB] 100s Get:270 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.3.0-1 [22.4 kB] 100s Get:271 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.3.0-1 [34.5 kB] 100s Get:272 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.3.0-1 [6594 B] 100s Get:273 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.3.0-1 [13.4 kB] 100s Get:274 http://ftpmaster.internal/ubuntu plucky/main armhf libnvme1t64 armhf 1.11.1-2 [73.6 kB] 100s Get:275 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.3.0-1 [17.7 kB] 100s Get:276 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.3.0-1 [16.6 kB] 100s Get:277 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.3.0-1 [9010 B] 100s Get:278 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.3.0-1 [44.4 kB] 100s Get:279 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-8 [26.3 kB] 100s Get:280 http://ftpmaster.internal/ubuntu plucky/main armhf libgstreamer1.0-0 armhf 1.25.50-1 [1164 kB] 100s Get:281 http://ftpmaster.internal/ubuntu plucky/main armhf libgudev-1.0-0 armhf 1:238-6 [13.7 kB] 100s Get:282 http://ftpmaster.internal/ubuntu plucky/main armhf libicu76 armhf 76.1-1ubuntu2 [10.8 MB] 101s Get:283 http://ftpmaster.internal/ubuntu plucky/main armhf libsasl2-modules armhf 2.1.28+dfsg1-8build1 [62.7 kB] 101s Get:284 http://ftpmaster.internal/ubuntu plucky/main armhf udisks2 armhf 2.10.1-11ubuntu2 [278 kB] 101s Get:285 http://ftpmaster.internal/ubuntu plucky/main armhf libudisks2-0 armhf 2.10.1-11ubuntu2 [142 kB] 101s Get:286 http://ftpmaster.internal/ubuntu plucky/main armhf libwrap0 armhf 7.6.q-35 [45.6 kB] 101s Get:287 http://ftpmaster.internal/ubuntu plucky/main armhf linux-headers-6.12.0-15 all 6.12.0-15.15 [14.1 MB] 101s Get:288 http://ftpmaster.internal/ubuntu plucky/main armhf linux-headers-6.12.0-15-generic armhf 6.12.0-15.15 [1414 kB] 101s Get:289 http://ftpmaster.internal/ubuntu plucky/main armhf linux-headers-generic armhf 6.12.0-15.15+1 [10.8 kB] 101s Get:290 http://ftpmaster.internal/ubuntu plucky/main armhf packagekit-tools armhf 1.3.0-3build1 [28.0 kB] 101s Get:291 http://ftpmaster.internal/ubuntu plucky/main armhf packagekit armhf 1.3.0-3build1 [431 kB] 101s Get:292 http://ftpmaster.internal/ubuntu plucky/main armhf pollinate all 4.33-4ubuntu2 [12.4 kB] 101s Get:293 http://ftpmaster.internal/ubuntu plucky/main armhf python3-babel all 2.17.0-1 [101 kB] 101s Get:294 http://ftpmaster.internal/ubuntu plucky/main armhf python-babel-localedata all 2.17.0-1 [6678 kB] 102s Get:295 http://ftpmaster.internal/ubuntu plucky/main armhf python3-certifi all 2025.1.31+ds-1 [9816 B] 102s Get:296 http://ftpmaster.internal/ubuntu plucky/main armhf python3-chardet all 5.2.0+dfsg-2 [116 kB] 102s Get:297 http://ftpmaster.internal/ubuntu plucky/main armhf python3-idna all 3.10-1 [47.4 kB] 102s Get:298 http://ftpmaster.internal/ubuntu plucky/main armhf python3-more-itertools all 10.6.0-1 [57.7 kB] 102s Get:299 http://ftpmaster.internal/ubuntu plucky/main armhf python3-openssl all 25.0.0-1 [46.1 kB] 102s Get:300 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pkg-resources all 75.6.0-1 [144 kB] 102s Get:301 http://ftpmaster.internal/ubuntu plucky/main armhf python3-setuptools all 75.6.0-1 [645 kB] 102s Get:302 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.108 [16.5 kB] 102s Get:303 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.108 [30.9 kB] 102s Get:304 http://ftpmaster.internal/ubuntu plucky/main armhf python3-urllib3 all 2.3.0-1 [94.0 kB] 103s Get:305 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-2 [36.2 kB] 103s Get:306 http://ftpmaster.internal/ubuntu plucky/main armhf unattended-upgrades all 2.12ubuntu2 [55.0 kB] 103s Get:307 http://ftpmaster.internal/ubuntu plucky/main armhf xfsprogs armhf 6.12.0-1ubuntu1 [958 kB] 103s Get:308 http://ftpmaster.internal/ubuntu plucky/main armhf zstd armhf 1.5.6+dfsg-2 [690 kB] 103s Get:309 http://ftpmaster.internal/ubuntu plucky/main armhf cloud-init all 25.1~3geb1965a4-0ubuntu1 [2102 B] 103s Get:310 http://ftpmaster.internal/ubuntu plucky/main armhf kpartx armhf 0.9.9-1ubuntu4 [35.0 kB] 103s Get:311 http://ftpmaster.internal/ubuntu plucky/main armhf multipath-tools armhf 0.9.9-1ubuntu4 [294 kB] 103s Preconfiguring packages ... 104s Fetched 135 MB in 9s (15.5 MB/s) 105s (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 ... 59970 files and directories currently installed.) 105s Preparing to unpack .../bash_5.2.37-1ubuntu1_armhf.deb ... 105s Unpacking bash (5.2.37-1ubuntu1) over (5.2.32-1ubuntu2) ... 105s Setting up bash (5.2.37-1ubuntu1) ... 105s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 105s (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 ... 59970 files and directories currently installed.) 105s Preparing to unpack .../bsdutils_1%3a2.40.2-14ubuntu1_armhf.deb ... 105s Unpacking bsdutils (1:2.40.2-14ubuntu1) over (1:2.40.2-1ubuntu1) ... 105s Setting up bsdutils (1:2.40.2-14ubuntu1) ... 105s (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 ... 59970 files and directories currently installed.) 105s Preparing to unpack .../coreutils_9.5-1ubuntu1_armhf.deb ... 105s Unpacking coreutils (9.5-1ubuntu1) over (9.4-3.1ubuntu1) ... 105s Setting up coreutils (9.5-1ubuntu1) ... 105s (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 ... 59970 files and directories currently installed.) 105s Preparing to unpack .../dash_0.5.12-12ubuntu1_armhf.deb ... 105s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 105s Setting up dash (0.5.12-12ubuntu1) ... 105s (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 ... 59970 files and directories currently installed.) 105s Preparing to unpack .../diffutils_1%3a3.10-2_armhf.deb ... 105s Unpacking diffutils (1:3.10-2) over (1:3.10-1build1) ... 105s Setting up diffutils (1:3.10-2) ... 105s Selecting previously unselected package gcc-15-base:armhf. 105s (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 ... 59970 files and directories currently installed.) 105s Preparing to unpack .../gcc-15-base_15-20250213-1ubuntu1_armhf.deb ... 105s Unpacking gcc-15-base:armhf (15-20250213-1ubuntu1) ... 105s Setting up gcc-15-base:armhf (15-20250213-1ubuntu1) ... 105s (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 ... 59975 files and directories currently installed.) 105s Preparing to unpack .../libgcc-s1_15-20250213-1ubuntu1_armhf.deb ... 105s Unpacking libgcc-s1:armhf (15-20250213-1ubuntu1) over (14.2.0-8ubuntu1) ... 105s Setting up libgcc-s1:armhf (15-20250213-1ubuntu1) ... 105s (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 ... 59975 files and directories currently installed.) 105s Preparing to unpack .../libc6_2.40-4ubuntu1_armhf.deb ... 106s Unpacking libc6:armhf (2.40-4ubuntu1) over (2.40-1ubuntu3) ... 106s Setting up libc6:armhf (2.40-4ubuntu1) ... 106s (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 ... 59975 files and directories currently installed.) 106s Preparing to unpack .../libxxhash0_0.8.3-2_armhf.deb ... 106s Unpacking libxxhash0:armhf (0.8.3-2) over (0.8.2-2build1) ... 106s Setting up libxxhash0:armhf (0.8.3-2) ... 106s (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 ... 59975 files and directories currently installed.) 106s Preparing to unpack .../liblz4-1_1.10.0-3_armhf.deb ... 106s Unpacking liblz4-1:armhf (1.10.0-3) over (1.9.4-3) ... 106s Setting up liblz4-1:armhf (1.10.0-3) ... 106s (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 ... 59975 files and directories currently installed.) 106s Preparing to unpack .../libssl3t64_3.4.0-1ubuntu2_armhf.deb ... 106s Unpacking libssl3t64:armhf (3.4.0-1ubuntu2) over (3.3.1-2ubuntu2) ... 106s Selecting previously unselected package openssl-provider-legacy. 106s Preparing to unpack .../openssl-provider-legacy_3.4.0-1ubuntu2_armhf.deb ... 106s Unpacking openssl-provider-legacy (3.4.0-1ubuntu2) ... 106s Setting up libssl3t64:armhf (3.4.0-1ubuntu2) ... 106s Setting up openssl-provider-legacy (3.4.0-1ubuntu2) ... 106s (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 ... 59978 files and directories currently installed.) 106s Preparing to unpack .../libzstd1_1.5.6+dfsg-2_armhf.deb ... 106s Unpacking libzstd1:armhf (1.5.6+dfsg-2) over (1.5.6+dfsg-1) ... 106s Setting up libzstd1:armhf (1.5.6+dfsg-2) ... 106s (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 ... 59978 files and directories currently installed.) 106s Preparing to unpack .../libstdc++6_15-20250213-1ubuntu1_armhf.deb ... 106s Unpacking libstdc++6:armhf (15-20250213-1ubuntu1) over (14.2.0-8ubuntu1) ... 106s Setting up libstdc++6:armhf (15-20250213-1ubuntu1) ... 106s (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 ... 59978 files and directories currently installed.) 106s Preparing to unpack .../0-systemd-timesyncd_257.2-3ubuntu1_armhf.deb ... 106s Unpacking systemd-timesyncd (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 106s Preparing to unpack .../1-dbus-session-bus-common_1.16.0-1ubuntu1_all.deb ... 106s Unpacking dbus-session-bus-common (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 106s Preparing to unpack .../2-systemd-sysv_257.2-3ubuntu1_armhf.deb ... 106s Unpacking systemd-sysv (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 107s Preparing to unpack .../3-libpam-systemd_257.2-3ubuntu1_armhf.deb ... 107s Unpacking libpam-systemd:armhf (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 107s Preparing to unpack .../4-dbus-user-session_1.16.0-1ubuntu1_armhf.deb ... 107s Unpacking dbus-user-session (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 107s Preparing to unpack .../5-libapparmor1_4.1.0~beta1-0ubuntu5_armhf.deb ... 107s Unpacking libapparmor1:armhf (4.1.0~beta1-0ubuntu5) over (4.1.0~beta1-0ubuntu4) ... 107s Preparing to unpack .../6-libcap-ng0_0.8.5-4_armhf.deb ... 107s Unpacking libcap-ng0:armhf (0.8.5-4) over (0.8.5-3build1) ... 107s Setting up libcap-ng0:armhf (0.8.5-4) ... 107s (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 ... 59979 files and directories currently installed.) 107s Preparing to unpack .../libselinux1_3.7-3ubuntu2_armhf.deb ... 107s Unpacking libselinux1:armhf (3.7-3ubuntu2) over (3.7-3ubuntu1) ... 107s Setting up libselinux1:armhf (3.7-3ubuntu2) ... 107s (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 ... 59979 files and directories currently installed.) 107s Preparing to unpack .../0-dbus-system-bus-common_1.16.0-1ubuntu1_all.deb ... 107s Unpacking dbus-system-bus-common (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 107s Preparing to unpack .../1-dbus-bin_1.16.0-1ubuntu1_armhf.deb ... 107s Unpacking dbus-bin (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 107s Preparing to unpack .../2-dbus_1.16.0-1ubuntu1_armhf.deb ... 107s Unpacking dbus (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 107s Preparing to unpack .../3-dbus-daemon_1.16.0-1ubuntu1_armhf.deb ... 107s Unpacking dbus-daemon (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 107s Preparing to unpack .../4-libdbus-1-3_1.16.0-1ubuntu1_armhf.deb ... 107s Unpacking libdbus-1-3:armhf (1.16.0-1ubuntu1) over (1.14.10-4ubuntu5) ... 108s Preparing to unpack .../5-systemd-resolved_257.2-3ubuntu1_armhf.deb ... 108s Unpacking systemd-resolved (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 108s Preparing to unpack .../6-systemd-cryptsetup_257.2-3ubuntu1_armhf.deb ... 108s Unpacking systemd-cryptsetup (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 108s Preparing to unpack .../7-libncurses6_6.5+20250125-2_armhf.deb ... 108s Unpacking libncurses6:armhf (6.5+20250125-2) over (6.5-2) ... 108s Preparing to unpack .../8-libncursesw6_6.5+20250125-2_armhf.deb ... 108s Unpacking libncursesw6:armhf (6.5+20250125-2) over (6.5-2) ... 108s Preparing to unpack .../9-libtinfo6_6.5+20250125-2_armhf.deb ... 108s Unpacking libtinfo6:armhf (6.5+20250125-2) over (6.5-2) ... 108s Setting up libtinfo6:armhf (6.5+20250125-2) ... 108s (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 ... 59979 files and directories currently installed.) 108s Preparing to unpack .../bsdextrautils_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking bsdextrautils (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Preparing to unpack .../eject_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking eject (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Preparing to unpack .../fdisk_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking fdisk (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Preparing to unpack .../libblkid1_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking libblkid1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Setting up libblkid1:armhf (2.40.2-14ubuntu1) ... 108s (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 ... 59975 files and directories currently installed.) 108s Preparing to unpack .../libmount1_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking libmount1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Setting up libmount1:armhf (2.40.2-14ubuntu1) ... 108s (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 ... 59975 files and directories currently installed.) 108s Preparing to unpack .../libsmartcols1_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking libsmartcols1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Setting up libsmartcols1:armhf (2.40.2-14ubuntu1) ... 108s (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 ... 59975 files and directories currently installed.) 108s Preparing to unpack .../libuuid1_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking libuuid1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Setting up libuuid1:armhf (2.40.2-14ubuntu1) ... 108s (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 ... 59975 files and directories currently installed.) 108s Preparing to unpack .../util-linux_2.40.2-14ubuntu1_armhf.deb ... 108s Unpacking util-linux (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 108s Setting up util-linux (2.40.2-14ubuntu1) ... 108s fstrim.service is a disabled or a static unit not running, not starting it. 109s (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 ... 59968 files and directories currently installed.) 109s Preparing to unpack .../0-uuid-runtime_2.40.2-14ubuntu1_armhf.deb ... 109s Unpacking uuid-runtime (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 109s Preparing to unpack .../1-libfdisk1_2.40.2-14ubuntu1_armhf.deb ... 109s Unpacking libfdisk1:armhf (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 109s Preparing to unpack .../2-mount_2.40.2-14ubuntu1_armhf.deb ... 109s Unpacking mount (2.40.2-14ubuntu1) over (2.40.2-1ubuntu1) ... 109s Preparing to unpack .../3-readline-common_8.2-6_all.deb ... 109s Unpacking readline-common (8.2-6) over (8.2-5) ... 109s Preparing to unpack .../4-libreadline8t64_8.2-6_armhf.deb ... 109s Leaving 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' 109s Leaving 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' 109s Leaving 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' 109s Leaving 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' 109s Unpacking libreadline8t64:armhf (8.2-6) over (8.2-5) ... 109s Preparing to unpack .../5-libcrypt1_1%3a4.4.38-1_armhf.deb ... 109s Unpacking libcrypt1:armhf (1:4.4.38-1) over (1:4.4.36-5) ... 109s Setting up libcrypt1:armhf (1:4.4.38-1) ... 109s (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 ... 59968 files and directories currently installed.) 109s Preparing to unpack .../libsystemd-shared_257.2-3ubuntu1_armhf.deb ... 109s Unpacking libsystemd-shared:armhf (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 109s Setting up libsystemd-shared:armhf (257.2-3ubuntu1) ... 109s (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 ... 59968 files and directories currently installed.) 109s Preparing to unpack .../systemd_257.2-3ubuntu1_armhf.deb ... 109s Unpacking systemd (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 109s Preparing to unpack .../udev_257.2-3ubuntu1_armhf.deb ... 109s Unpacking udev (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 109s Preparing to unpack .../libnss-systemd_257.2-3ubuntu1_armhf.deb ... 109s Unpacking libnss-systemd:armhf (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 109s Preparing to unpack .../libudev1_257.2-3ubuntu1_armhf.deb ... 109s Unpacking libudev1:armhf (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 109s Setting up libudev1:armhf (257.2-3ubuntu1) ... 110s (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 ... 59962 files and directories currently installed.) 110s Preparing to unpack .../libsystemd0_257.2-3ubuntu1_armhf.deb ... 110s Unpacking libsystemd0:armhf (257.2-3ubuntu1) over (256.5-2ubuntu4) ... 110s Setting up libsystemd0:armhf (257.2-3ubuntu1) ... 110s (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 ... 59962 files and directories currently installed.) 110s Preparing to unpack .../libapt-pkg6.0t64_2.9.29_armhf.deb ... 110s Unpacking libapt-pkg6.0t64:armhf (2.9.29) over (2.9.14ubuntu1) ... 110s Setting up libapt-pkg6.0t64:armhf (2.9.29) ... 110s (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 ... 59962 files and directories currently installed.) 110s Preparing to unpack .../tar_1.35+dfsg-3.1_armhf.deb ... 110s Unpacking tar (1.35+dfsg-3.1) over (1.35+dfsg-3build1) ... 110s Setting up tar (1.35+dfsg-3.1) ... 110s (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 ... 59962 files and directories currently installed.) 110s Preparing to unpack .../dpkg_1.22.11ubuntu4_armhf.deb ... 110s Unpacking dpkg (1.22.11ubuntu4) over (1.22.11ubuntu3) ... 110s Setting up dpkg (1.22.11ubuntu4) ... 110s (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 ... 59962 files and directories currently installed.) 110s Preparing to unpack .../gzip_1.13-1ubuntu2_armhf.deb ... 110s Unpacking gzip (1.13-1ubuntu2) over (1.12-1.1ubuntu1) ... 110s Setting up gzip (1.13-1ubuntu2) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../ncurses-bin_6.5+20250125-2_armhf.deb ... 111s Unpacking ncurses-bin (6.5+20250125-2) over (6.5-2) ... 111s Setting up ncurses-bin (6.5+20250125-2) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../libdebconfclient0_0.274ubuntu1_armhf.deb ... 111s Unpacking libdebconfclient0:armhf (0.274ubuntu1) over (0.272ubuntu1) ... 111s Setting up libdebconfclient0:armhf (0.274ubuntu1) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../base-passwd_3.6.6_armhf.deb ... 111s Unpacking base-passwd (3.6.6) over (3.6.5) ... 111s Setting up base-passwd (3.6.6) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../init-system-helpers_1.68_all.deb ... 111s Unpacking init-system-helpers (1.68) over (1.67ubuntu1) ... 111s Setting up init-system-helpers (1.68) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../libc-bin_2.40-4ubuntu1_armhf.deb ... 111s Unpacking libc-bin (2.40-4ubuntu1) over (2.40-1ubuntu3) ... 111s Setting up libc-bin (2.40-4ubuntu1) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../ncurses-base_6.5+20250125-2_all.deb ... 111s Unpacking ncurses-base (6.5+20250125-2) over (6.5-2) ... 111s Setting up ncurses-base (6.5+20250125-2) ... 111s (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 ... 59962 files and directories currently installed.) 111s Preparing to unpack .../ncurses-term_6.5+20250125-2_all.deb ... 111s Unpacking ncurses-term (6.5+20250125-2) over (6.5-2) ... 112s Selecting previously unselected package libapt-pkg7.0:armhf. 112s Preparing to unpack .../libapt-pkg7.0_2.9.30_armhf.deb ... 112s Unpacking libapt-pkg7.0:armhf (2.9.30) ... 112s Setting up libapt-pkg7.0:armhf (2.9.30) ... 112s (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 ... 60019 files and directories currently installed.) 112s Preparing to unpack .../archives/apt_2.9.30_armhf.deb ... 112s Unpacking apt (2.9.30) over (2.9.14ubuntu1) ... 112s Setting up apt (2.9.30) ... 113s (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 ... 60021 files and directories currently installed.) 113s Preparing to unpack .../apt-utils_2.9.30_armhf.deb ... 113s Unpacking apt-utils (2.9.30) over (2.9.14ubuntu1) ... 113s Preparing to unpack .../libgpg-error-l10n_1.51-3_all.deb ... 113s Unpacking libgpg-error-l10n (1.51-3) over (1.50-4) ... 113s Preparing to unpack .../libgpg-error0_1.51-3_armhf.deb ... 113s Unpacking libgpg-error0:armhf (1.51-3) over (1.50-4) ... 113s Setting up libgpg-error0:armhf (1.51-3) ... 113s (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 ... 60021 files and directories currently installed.) 113s Preparing to unpack .../libnpth0t64_1.8-2_armhf.deb ... 113s Unpacking libnpth0t64:armhf (1.8-2) over (1.6-3.1build1) ... 113s Setting up libnpth0t64:armhf (1.8-2) ... 113s (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 ... 60021 files and directories currently installed.) 113s Preparing to unpack .../00-gpg-wks-client_2.4.4-2ubuntu22_armhf.deb ... 113s Unpacking gpg-wks-client (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 113s Preparing to unpack .../01-dirmngr_2.4.4-2ubuntu22_armhf.deb ... 113s Unpacking dirmngr (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 113s Preparing to unpack .../02-gpgsm_2.4.4-2ubuntu22_armhf.deb ... 113s Unpacking gpgsm (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 113s Preparing to unpack .../03-gnupg-utils_2.4.4-2ubuntu22_armhf.deb ... 113s Unpacking gnupg-utils (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 113s Preparing to unpack .../04-gpg-agent_2.4.4-2ubuntu22_armhf.deb ... 113s Unpacking gpg-agent (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 114s Preparing to unpack .../05-gpg_2.4.4-2ubuntu22_armhf.deb ... 114s Unpacking gpg (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 114s Preparing to unpack .../06-gpgconf_2.4.4-2ubuntu22_armhf.deb ... 114s Unpacking gpgconf (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 114s Preparing to unpack .../07-gnupg_2.4.4-2ubuntu22_all.deb ... 114s Unpacking gnupg (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 114s Preparing to unpack .../08-keyboxd_2.4.4-2ubuntu22_armhf.deb ... 114s Unpacking keyboxd (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 114s Preparing to unpack .../09-pinentry-curses_1.3.1-2ubuntu2_armhf.deb ... 114s Unpacking pinentry-curses (1.3.1-2ubuntu2) over (1.3.1-0ubuntu2) ... 114s Preparing to unpack .../10-libnettle8t64_3.10.1-1_armhf.deb ... 114s Unpacking libnettle8t64:armhf (3.10.1-1) over (3.10-1) ... 114s Setting up libnettle8t64:armhf (3.10.1-1) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libhogweed6t64_3.10.1-1_armhf.deb ... 114s Unpacking libhogweed6t64:armhf (3.10.1-1) over (3.10-1) ... 114s Setting up libhogweed6t64:armhf (3.10.1-1) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libffi8_3.4.7-1_armhf.deb ... 114s Unpacking libffi8:armhf (3.4.7-1) over (3.4.6-1build1) ... 114s Setting up libffi8:armhf (3.4.7-1) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libp11-kit0_0.25.5-2ubuntu3_armhf.deb ... 114s Unpacking libp11-kit0:armhf (0.25.5-2ubuntu3) over (0.25.5-2ubuntu1) ... 114s Setting up libp11-kit0:armhf (0.25.5-2ubuntu3) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libtasn1-6_4.20.0-2_armhf.deb ... 114s Unpacking libtasn1-6:armhf (4.20.0-2) over (4.19.0-3build1) ... 114s Setting up libtasn1-6:armhf (4.20.0-2) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libunistring5_1.3-1_armhf.deb ... 114s Unpacking libunistring5:armhf (1.3-1) over (1.2-1) ... 114s Setting up libunistring5:armhf (1.3-1) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libgnutls30t64_3.8.9-2ubuntu1_armhf.deb ... 114s Unpacking libgnutls30t64:armhf (3.8.9-2ubuntu1) over (3.8.8-2ubuntu1) ... 114s Setting up libgnutls30t64:armhf (3.8.9-2ubuntu1) ... 114s (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 ... 60021 files and directories currently installed.) 114s Preparing to unpack .../libsasl2-modules-db_2.1.28+dfsg1-8build1_armhf.deb ... 114s Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8build1) over (2.1.28+dfsg1-8) ... 114s Preparing to unpack .../libsasl2-2_2.1.28+dfsg1-8build1_armhf.deb ... 114s Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8build1) over (2.1.28+dfsg1-8) ... 115s Preparing to unpack .../libldap-common_2.6.9+dfsg-1~exp2ubuntu1_all.deb ... 115s Unpacking libldap-common (2.6.9+dfsg-1~exp2ubuntu1) over (2.6.8+dfsg-1~exp4ubuntu3) ... 115s Preparing to unpack .../libldap2_2.6.9+dfsg-1~exp2ubuntu1_armhf.deb ... 115s Unpacking libldap2:armhf (2.6.9+dfsg-1~exp2ubuntu1) over (2.6.8+dfsg-1~exp4ubuntu3) ... 115s Preparing to unpack .../gpgv_2.4.4-2ubuntu22_armhf.deb ... 115s Unpacking gpgv (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 115s Setting up gpgv (2.4.4-2ubuntu22) ... 115s (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 ... 60020 files and directories currently installed.) 115s Preparing to unpack .../0-e2fsprogs-l10n_1.47.2-1ubuntu1_all.deb ... 115s Unpacking e2fsprogs-l10n (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 115s Preparing to unpack .../1-logsave_1.47.2-1ubuntu1_armhf.deb ... 115s Unpacking logsave (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 115s Preparing to unpack .../2-ubuntu-minimal_1.547_armhf.deb ... 115s Unpacking ubuntu-minimal (1.547) over (1.544) ... 115s Preparing to unpack .../3-initramfs-tools_0.145ubuntu2_all.deb ... 115s Unpacking initramfs-tools (0.145ubuntu2) over (0.142ubuntu35) ... 115s Preparing to unpack .../4-initramfs-tools-core_0.145ubuntu2_all.deb ... 115s Unpacking initramfs-tools-core (0.145ubuntu2) over (0.142ubuntu35) ... 115s Preparing to unpack .../5-libext2fs2t64_1.47.2-1ubuntu1_armhf.deb ... 115s Leaving 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2 to /lib/arm-linux-gnueabihf/libe2p.so.2.usr-is-merged by libext2fs2t64' 115s Leaving 'diversion of /lib/arm-linux-gnueabihf/libe2p.so.2.3 to /lib/arm-linux-gnueabihf/libe2p.so.2.3.usr-is-merged by libext2fs2t64' 115s Leaving 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2 to /lib/arm-linux-gnueabihf/libext2fs.so.2.usr-is-merged by libext2fs2t64' 115s Leaving 'diversion of /lib/arm-linux-gnueabihf/libext2fs.so.2.4 to /lib/arm-linux-gnueabihf/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' 115s Unpacking libext2fs2t64:armhf (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 115s Setting up libext2fs2t64:armhf (1.47.2-1ubuntu1) ... 115s (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 ... 60020 files and directories currently installed.) 115s Preparing to unpack .../e2fsprogs_1.47.2-1ubuntu1_armhf.deb ... 115s Unpacking e2fsprogs (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 115s Preparing to unpack .../console-setup-linux_1.226ubuntu3_all.deb ... 115s Unpacking console-setup-linux (1.226ubuntu3) over (1.226ubuntu2) ... 115s Preparing to unpack .../console-setup_1.226ubuntu3_all.deb ... 115s Unpacking console-setup (1.226ubuntu3) over (1.226ubuntu2) ... 115s Preparing to unpack .../keyboard-configuration_1.226ubuntu3_all.deb ... 115s Unpacking keyboard-configuration (1.226ubuntu3) over (1.226ubuntu2) ... 115s Preparing to unpack .../dhcpcd-base_1%3a10.1.0-7_armhf.deb ... 115s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-2) ... 115s Setting up libapparmor1:armhf (4.1.0~beta1-0ubuntu5) ... 115s Setting up mount (2.40.2-14ubuntu1) ... 115s Setting up systemd (257.2-3ubuntu1) ... 115s Installing new version of config file /etc/systemd/logind.conf ... 115s Installing new version of config file /etc/systemd/sleep.conf ... 115s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 115s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 116s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 116s Setting up systemd-sysv (257.2-3ubuntu1) ... 116s (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 ... 60019 files and directories currently installed.) 116s Preparing to unpack .../00-init_1.68_armhf.deb ... 116s Unpacking init (1.68) over (1.67ubuntu1) ... 116s Preparing to unpack .../01-libbpf1_1%3a1.5.0-2_armhf.deb ... 116s Unpacking libbpf1:armhf (1:1.5.0-2) over (1:1.5.0-1) ... 116s Preparing to unpack .../02-iptables_1.8.11-2ubuntu1_armhf.deb ... 116s Unpacking iptables (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 116s Preparing to unpack .../03-libip4tc2_1.8.11-2ubuntu1_armhf.deb ... 116s Unpacking libip4tc2:armhf (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 116s Preparing to unpack .../04-libip6tc2_1.8.11-2ubuntu1_armhf.deb ... 116s Unpacking libip6tc2:armhf (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 116s Preparing to unpack .../05-libnftnl11_1.2.8-1_armhf.deb ... 116s Unpacking libnftnl11:armhf (1.2.8-1) over (1.2.7-1) ... 116s Preparing to unpack .../06-libxtables12_1.8.11-2ubuntu1_armhf.deb ... 116s Unpacking libxtables12:armhf (1.8.11-2ubuntu1) over (1.8.10-3ubuntu2) ... 116s Preparing to unpack .../07-iproute2_6.13.0-1ubuntu1_armhf.deb ... 117s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 117s Preparing to unpack .../08-iputils-ping_3%3a20240905-1ubuntu1_armhf.deb ... 117s Unpacking iputils-ping (3:20240905-1ubuntu1) over (3:20240117-1build1) ... 117s Preparing to unpack .../09-locales_2.40-4ubuntu1_all.deb ... 117s Unpacking locales (2.40-4ubuntu1) over (2.40-1ubuntu3) ... 117s Selecting previously unselected package login.defs. 118s Preparing to unpack .../10-login.defs_1%3a4.16.0-7ubuntu1_all.deb ... 118s Unpacking login.defs (1:4.16.0-7ubuntu1) ... 118s Replacing files in old package login (1:4.15.3-3ubuntu2) ... 118s Setting up login.defs (1:4.16.0-7ubuntu1) ... 118s Installing new version of config file /etc/login.defs ... 118s (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 ... 60026 files and directories currently installed.) 118s Preparing to unpack .../0-login_1%3a4.16.0-2+really2.40.2-14ubuntu1_armhf.deb ... 118s Unpacking login (1:4.16.0-2+really2.40.2-14ubuntu1) over (1:4.15.3-3ubuntu2) ... 118s Preparing to unpack .../1-mawk_1.3.4.20250131-1_armhf.deb ... 118s Unpacking mawk (1.3.4.20250131-1) over (1.3.4.20240905-1) ... 118s Preparing to unpack .../2-netcat-openbsd_1.228-1_armhf.deb ... 118s Unpacking netcat-openbsd (1.228-1) over (1.226-1.1) ... 118s Selecting previously unselected package libpython3.13-minimal:armhf. 118s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-1_armhf.deb ... 118s Unpacking libpython3.13-minimal:armhf (3.13.2-1) ... 118s Selecting previously unselected package python3.13-minimal. 118s Preparing to unpack .../4-python3.13-minimal_3.13.2-1_armhf.deb ... 118s Unpacking python3.13-minimal (3.13.2-1) ... 118s Preparing to unpack .../5-python3-cryptography_43.0.0-1_armhf.deb ... 118s Unpacking python3-cryptography (43.0.0-1) over (42.0.5-2build1) ... 118s Setting up libpython3.13-minimal:armhf (3.13.2-1) ... 118s Setting up python3.13-minimal (3.13.2-1) ... 119s (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 ... 60308 files and directories currently installed.) 119s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_armhf.deb ... 119s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.6-0ubuntu1) ... 119s Setting up python3-minimal (3.13.1-1~exp2) ... 119s (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 ... 60308 files and directories currently installed.) 119s Preparing to unpack .../00-python3_3.13.1-1~exp2_armhf.deb ... 119s Unpacking python3 (3.13.1-1~exp2) over (3.12.6-0ubuntu1) ... 119s Selecting previously unselected package python3-bcrypt. 119s Preparing to unpack .../01-python3-bcrypt_4.2.0-2.1_armhf.deb ... 119s Unpacking python3-bcrypt (4.2.0-2.1) ... 119s Preparing to unpack .../02-tzdata_2025a-2ubuntu1_all.deb ... 119s Unpacking tzdata (2025a-2ubuntu1) over (2024b-1ubuntu2) ... 119s Selecting previously unselected package libpython3.13-stdlib:armhf. 119s Preparing to unpack .../03-libpython3.13-stdlib_3.13.2-1_armhf.deb ... 119s Unpacking libpython3.13-stdlib:armhf (3.13.2-1) ... 119s Selecting previously unselected package python3.13. 119s Preparing to unpack .../04-python3.13_3.13.2-1_armhf.deb ... 119s Unpacking python3.13 (3.13.2-1) ... 119s Preparing to unpack .../05-libpython3-stdlib_3.13.1-1~exp2_armhf.deb ... 119s Unpacking libpython3-stdlib:armhf (3.13.1-1~exp2) over (3.12.6-0ubuntu1) ... 119s Preparing to unpack .../06-gir1.2-girepository-2.0_1.82.0-4_armhf.deb ... 119s Unpacking gir1.2-girepository-2.0:armhf (1.82.0-4) over (1.82.0-2) ... 119s Preparing to unpack .../07-gir1.2-glib-2.0_2.83.3-2_armhf.deb ... 119s Unpacking gir1.2-glib-2.0:armhf (2.83.3-2) over (2.82.2-3) ... 119s Preparing to unpack .../08-libgirepository-1.0-1_1.82.0-4_armhf.deb ... 119s Unpacking libgirepository-1.0-1:armhf (1.82.0-4) over (1.82.0-2) ... 119s Preparing to unpack .../09-libglib2.0-data_2.83.3-2_all.deb ... 119s Unpacking libglib2.0-data (2.83.3-2) over (2.82.2-3) ... 119s Preparing to unpack .../10-libglib2.0-bin_2.83.3-2_armhf.deb ... 119s Unpacking libglib2.0-bin (2.83.3-2) over (2.82.2-3) ... 119s Preparing to unpack .../11-libatomic1_15-20250213-1ubuntu1_armhf.deb ... 119s Unpacking libatomic1:armhf (15-20250213-1ubuntu1) over (14.2.0-8ubuntu1) ... 119s Preparing to unpack .../12-libglib2.0-0t64_2.83.3-2_armhf.deb ... 119s Unpacking libglib2.0-0t64:armhf (2.83.3-2) over (2.82.2-3) ... 119s Preparing to unpack .../13-netplan-generator_1.1.2-2ubuntu1_armhf.deb ... 119s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 119s Unpacking netplan-generator (1.1.2-2ubuntu1) over (1.1.1-1) ... 119s Preparing to unpack .../14-libyaml-0-2_0.2.5-2_armhf.deb ... 119s Unpacking libyaml-0-2:armhf (0.2.5-2) over (0.2.5-1build1) ... 120s Preparing to unpack .../15-python3-netplan_1.1.2-2ubuntu1_armhf.deb ... 120s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 120s for fn in glob1(directory, "%s.*" % fname): 120s Unpacking python3-netplan (1.1.2-2ubuntu1) over (1.1.1-1) ... 120s Preparing to unpack .../16-netplan.io_1.1.2-2ubuntu1_armhf.deb ... 120s Unpacking netplan.io (1.1.2-2ubuntu1) over (1.1.1-1) ... 120s Preparing to unpack .../17-libnetplan1_1.1.2-2ubuntu1_armhf.deb ... 120s Unpacking libnetplan1:armhf (1.1.2-2ubuntu1) over (1.1.1-1) ... 120s Preparing to unpack .../18-ethtool_1%3a6.11-1_armhf.deb ... 120s Unpacking ethtool (1:6.11-1) over (1:6.10-1) ... 120s Preparing to unpack .../19-libsemanage-common_3.7-2.1_all.deb ... 120s Unpacking libsemanage-common (3.7-2.1) over (3.7-2build1) ... 120s Setting up libsemanage-common (3.7-2.1) ... 120s (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 ... 60731 files and directories currently installed.) 120s Preparing to unpack .../libsemanage2_3.7-2.1_armhf.deb ... 120s Unpacking libsemanage2:armhf (3.7-2.1) over (3.7-2build1) ... 120s Setting up libsemanage2:armhf (3.7-2.1) ... 120s (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 ... 60731 files and directories currently installed.) 120s Preparing to unpack .../passwd_1%3a4.16.0-7ubuntu1_armhf.deb ... 120s Unpacking passwd (1:4.16.0-7ubuntu1) over (1:4.15.3-3ubuntu2) ... 120s Setting up passwd (1:4.16.0-7ubuntu1) ... 120s (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 ... 60766 files and directories currently installed.) 120s Preparing to unpack .../000-python3-newt_0.52.24-4ubuntu1_armhf.deb ... 120s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 120s for fn in glob1(directory, "%s.*" % fname): 120s Unpacking python3-newt:armhf (0.52.24-4ubuntu1) over (0.52.24-2ubuntu4) ... 120s Preparing to unpack .../001-libnewt0.52_0.52.24-4ubuntu1_armhf.deb ... 120s Unpacking libnewt0.52:armhf (0.52.24-4ubuntu1) over (0.52.24-2ubuntu4) ... 120s Preparing to unpack .../002-whiptail_0.52.24-4ubuntu1_armhf.deb ... 120s Unpacking whiptail (0.52.24-4ubuntu1) over (0.52.24-2ubuntu4) ... 120s Preparing to unpack .../003-dracut-install_106-2ubuntu1_armhf.deb ... 120s Unpacking dracut-install (106-2ubuntu1) over (105-2ubuntu3) ... 120s Preparing to unpack .../004-initramfs-tools-bin_0.145ubuntu2_armhf.deb ... 120s Unpacking initramfs-tools-bin (0.145ubuntu2) over (0.142ubuntu35) ... 120s Preparing to unpack .../005-busybox-initramfs_1%3a1.37.0-4ubuntu1_armhf.deb ... 120s Unpacking busybox-initramfs (1:1.37.0-4ubuntu1) over (1:1.36.1-9ubuntu1) ... 120s Preparing to unpack .../006-python3.12_3.12.9-1_armhf.deb ... 120s Unpacking python3.12 (3.12.9-1) over (3.12.7-3) ... 120s Preparing to unpack .../007-libpython3.12-stdlib_3.12.9-1_armhf.deb ... 121s Unpacking libpython3.12-stdlib:armhf (3.12.9-1) over (3.12.7-3) ... 121s Preparing to unpack .../008-python3.12-minimal_3.12.9-1_armhf.deb ... 121s Unpacking python3.12-minimal (3.12.9-1) over (3.12.7-3) ... 121s Preparing to unpack .../009-libpython3.12-minimal_3.12.9-1_armhf.deb ... 121s Unpacking libpython3.12-minimal:armhf (3.12.9-1) over (3.12.7-3) ... 121s Preparing to unpack .../010-cron_3.0pl1-192ubuntu1_armhf.deb ... 121s Unpacking cron (3.0pl1-192ubuntu1) over (3.0pl1-189ubuntu1) ... 121s Preparing to unpack .../011-rsync_3.4.1-0syncable1_armhf.deb ... 121s Unpacking rsync (3.4.1-0syncable1) over (3.3.0-1) ... 121s Preparing to unpack .../012-python-apt-common_2.9.8_all.deb ... 121s Unpacking python-apt-common (2.9.8) over (2.9.0ubuntu2) ... 121s Preparing to unpack .../013-python3-apt_2.9.8_armhf.deb ... 121s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 121s for fn in glob1(directory, "%s.*" % fname): 121s Unpacking python3-apt (2.9.8) over (2.9.0ubuntu2) ... 121s Preparing to unpack .../014-python3-lazr.uri_1.0.6-5_all.deb ... 121s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 121s for fn in glob1(directory, "%s.*" % fname): 121s Unpacking python3-lazr.uri (1.0.6-5) over (1.0.6-4) ... 121s Preparing to unpack .../015-python3-launchpadlib_2.1.0-1_all.deb ... 121s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 121s for fn in glob1(directory, "%s.*" % fname): 121s Unpacking python3-launchpadlib (2.1.0-1) over (2.0.0-1) ... 121s Preparing to unpack .../016-python3-problem-report_2.31.0-0ubuntu5_all.deb ... 121s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 121s for fn in glob1(directory, "%s.*" % fname): 121s Unpacking python3-problem-report (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 121s Preparing to unpack .../017-python3-apport_2.31.0-0ubuntu5_all.deb ... 122s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 122s for fn in glob1(directory, "%s.*" % fname): 122s Unpacking python3-apport (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 122s Preparing to unpack .../018-python3-gi_3.50.0-4_armhf.deb ... 122s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 122s for fn in glob1(directory, "%s.*" % fname): 122s Unpacking python3-gi (3.50.0-4) over (3.50.0-3build1) ... 122s Preparing to unpack .../019-apport-core-dump-handler_2.31.0-0ubuntu5_all.deb ... 122s Unpacking apport-core-dump-handler (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 122s Preparing to unpack .../020-apport_2.31.0-0ubuntu5_all.deb ... 122s Unpacking apport (2.31.0-0ubuntu5) over (2.30.0-0ubuntu5) ... 122s Preparing to unpack .../021-gcc-14-base_14.2.0-17ubuntu1_armhf.deb ... 122s Unpacking gcc-14-base:armhf (14.2.0-17ubuntu1) over (14.2.0-8ubuntu1) ... 122s Preparing to unpack .../022-libcom-err2_1.47.2-1ubuntu1_armhf.deb ... 122s Unpacking libcom-err2:armhf (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 122s Preparing to unpack .../023-libss2_1.47.2-1ubuntu1_armhf.deb ... 122s Unpacking libss2:armhf (1.47.2-1ubuntu1) over (1.47.1-1ubuntu1) ... 122s Preparing to unpack .../024-openssl_3.4.0-1ubuntu2_armhf.deb ... 122s Unpacking openssl (3.4.0-1ubuntu2) over (3.3.1-2ubuntu2) ... 122s Preparing to unpack .../025-ca-certificates_20241223_all.deb ... 122s Unpacking ca-certificates (20241223) over (20240203) ... 122s Preparing to unpack .../026-distro-info_1.13_armhf.deb ... 122s Unpacking distro-info (1.13) over (1.12) ... 122s Preparing to unpack .../027-krb5-locales_1.21.3-4ubuntu1_all.deb ... 122s Unpacking krb5-locales (1.21.3-4ubuntu1) over (1.21.3-3) ... 122s Preparing to unpack .../028-libfribidi0_1.0.16-1_armhf.deb ... 122s Unpacking libfribidi0:armhf (1.0.16-1) over (1.0.15-1) ... 122s Preparing to unpack .../029-libgssapi-krb5-2_1.21.3-4ubuntu1_armhf.deb ... 122s Unpacking libgssapi-krb5-2:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 122s Preparing to unpack .../030-libkrb5-3_1.21.3-4ubuntu1_armhf.deb ... 122s Unpacking libkrb5-3:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 122s Preparing to unpack .../031-libkrb5support0_1.21.3-4ubuntu1_armhf.deb ... 122s Unpacking libkrb5support0:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 122s Preparing to unpack .../032-libk5crypto3_1.21.3-4ubuntu1_armhf.deb ... 122s Unpacking libk5crypto3:armhf (1.21.3-4ubuntu1) over (1.21.3-3) ... 122s Preparing to unpack .../033-libicu74_74.2-1ubuntu6_armhf.deb ... 122s Unpacking libicu74:armhf (74.2-1ubuntu6) over (74.2-1ubuntu4) ... 123s Preparing to unpack .../034-libxml2_2.12.7+dfsg+really2.9.14-0.2ubuntu3_armhf.deb ... 123s Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2ubuntu3) over (2.12.7+dfsg-3) ... 123s Preparing to unpack .../035-python3-pygments_2.18.0+dfsg-2_all.deb ... 123s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 123s for fn in glob1(directory, "%s.*" % fname): 123s Unpacking python3-pygments (2.18.0+dfsg-2) over (2.18.0+dfsg-1ubuntu1) ... 123s Preparing to unpack .../036-python3-rich_13.9.4-1_all.deb ... 123s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 123s for fn in glob1(directory, "%s.*" % fname): 123s Unpacking python3-rich (13.9.4-1) over (13.7.1-1) ... 123s Preparing to unpack .../037-ucf_3.0049_all.deb ... 123s Unpacking ucf (3.0049) over (3.0043+nmu1) ... 123s Preparing to unpack .../038-rsyslog_8.2412.0-2ubuntu1_armhf.deb ... 123s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2406.0-1ubuntu2) ... 123s Preparing to unpack .../039-apparmor_4.1.0~beta1-0ubuntu5_armhf.deb ... 124s Unpacking apparmor (4.1.0~beta1-0ubuntu5) over (4.1.0~beta1-0ubuntu4) ... 124s Preparing to unpack .../040-bash-completion_1%3a2.16.0-7_all.deb ... 124s Unpacking bash-completion (1:2.16.0-7) over (1:2.14.0-2) ... 125s Preparing to unpack .../041-libmaxminddb0_1.12.2-1_armhf.deb ... 125s Unpacking libmaxminddb0:armhf (1.12.2-1) over (1.11.0-1) ... 125s Preparing to unpack .../042-liburcu8t64_0.15.0-1_armhf.deb ... 125s Unpacking liburcu8t64:armhf (0.15.0-1) over (0.14.1-1) ... 125s Preparing to unpack .../043-bind9-dnsutils_1%3a9.20.0-2ubuntu4_armhf.deb ... 125s Unpacking bind9-dnsutils (1:9.20.0-2ubuntu4) over (1:9.20.0-2ubuntu3) ... 125s Preparing to unpack .../044-bind9-host_1%3a9.20.0-2ubuntu4_armhf.deb ... 125s Unpacking bind9-host (1:9.20.0-2ubuntu4) over (1:9.20.0-2ubuntu3) ... 125s Preparing to unpack .../045-bind9-libs_1%3a9.20.0-2ubuntu4_armhf.deb ... 125s Unpacking bind9-libs:armhf (1:9.20.0-2ubuntu4) over (1:9.20.0-2ubuntu3) ... 125s Preparing to unpack .../046-libedit2_3.1-20250104-1_armhf.deb ... 125s Unpacking libedit2:armhf (3.1-20250104-1) over (3.1-20240808-1) ... 125s Preparing to unpack .../047-busybox-static_1%3a1.37.0-4ubuntu1_armhf.deb ... 125s Unpacking busybox-static (1:1.37.0-4ubuntu1) over (1:1.36.1-9ubuntu1) ... 125s Preparing to unpack .../048-cron-daemon-common_3.0pl1-192ubuntu1_all.deb ... 125s Unpacking cron-daemon-common (3.0pl1-192ubuntu1) over (3.0pl1-189ubuntu1) ... 125s Preparing to unpack .../049-libdevmapper1.02.1_2%3a1.02.201-1ubuntu1_armhf.deb ... 125s Unpacking libdevmapper1.02.1:armhf (2:1.02.201-1ubuntu1) over (2:1.02.196-1ubuntu2) ... 125s Preparing to unpack .../050-dmsetup_2%3a1.02.201-1ubuntu1_armhf.deb ... 125s Unpacking dmsetup (2:1.02.201-1ubuntu1) over (2:1.02.196-1ubuntu2) ... 125s Preparing to unpack .../051-ed_1.21-1_armhf.deb ... 125s Unpacking ed (1.21-1) over (1.20.2-2) ... 125s Preparing to unpack .../052-gettext-base_0.23.1-1_armhf.deb ... 125s Unpacking gettext-base (0.23.1-1) over (0.22.5-2) ... 125s Preparing to unpack .../053-groff-base_1.23.0-7_armhf.deb ... 125s Unpacking groff-base (1.23.0-7) over (1.23.0-5) ... 125s Preparing to unpack .../054-libibverbs1_55.0-1ubuntu1_armhf.deb ... 125s Unpacking libibverbs1:armhf (55.0-1ubuntu1) over (52.0-2ubuntu1) ... 125s Preparing to unpack .../055-ibverbs-providers_55.0-1ubuntu1_armhf.deb ... 125s Unpacking ibverbs-providers:armhf (55.0-1ubuntu1) over (52.0-2ubuntu1) ... 125s Preparing to unpack .../056-iputils-tracepath_3%3a20240905-1ubuntu1_armhf.deb ... 125s Unpacking iputils-tracepath (3:20240905-1ubuntu1) over (3:20240117-1build1) ... 125s Preparing to unpack .../057-nftables_1.1.1-1build1_armhf.deb ... 125s Unpacking nftables (1.1.1-1build1) over (1.1.0-2) ... 125s Preparing to unpack .../058-libnftables1_1.1.1-1build1_armhf.deb ... 125s Unpacking libnftables1:armhf (1.1.1-1build1) over (1.1.0-2) ... 125s Preparing to unpack .../059-libpcap0.8t64_1.10.5-2ubuntu1_armhf.deb ... 125s Unpacking libpcap0.8t64:armhf (1.10.5-2ubuntu1) over (1.10.5-1ubuntu1) ... 125s Preparing to unpack .../060-libpng16-16t64_1.6.46-4_armhf.deb ... 125s Unpacking libpng16-16t64:armhf (1.6.46-4) over (1.6.44-2) ... 126s Preparing to unpack .../061-libtraceevent1-plugin_1%3a1.8.4-2_armhf.deb ... 126s Unpacking libtraceevent1-plugin:armhf (1:1.8.4-2) over (1:1.8.4-1) ... 126s Preparing to unpack .../062-libtraceevent1_1%3a1.8.4-2_armhf.deb ... 126s Unpacking libtraceevent1:armhf (1:1.8.4-2) over (1:1.8.4-1) ... 126s Preparing to unpack .../063-libusb-1.0-0_2%3a1.0.27-2_armhf.deb ... 126s Unpacking libusb-1.0-0:armhf (2:1.0.27-2) over (2:1.0.27-1) ... 126s Preparing to unpack .../064-libxdmcp6_1%3a1.1.5-1_armhf.deb ... 126s Unpacking libxdmcp6:armhf (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 126s Preparing to unpack .../065-libxkbcommon0_1.7.0-2_armhf.deb ... 126s Unpacking libxkbcommon0:armhf (1.7.0-2) over (1.7.0-1) ... 126s Preparing to unpack .../066-lshw_02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1_armhf.deb ... 126s Unpacking lshw (02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1) over (02.19.git.2021.06.19.996aaad9c7-2ubuntu2) ... 126s Preparing to unpack .../067-lsof_4.99.4+dfsg-1_armhf.deb ... 126s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 126s Preparing to unpack .../068-liblsof0_4.99.4+dfsg-1_armhf.deb ... 126s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 126s Preparing to unpack .../069-nano_8.3-1_armhf.deb ... 126s Unpacking nano (8.3-1) over (8.2-1) ... 126s Preparing to unpack .../070-pci.ids_0.0~2025.02.12-1_all.deb ... 126s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2024.10.24-1) ... 126s Preparing to unpack .../071-powermgmt-base_1.38_all.deb ... 126s Unpacking powermgmt-base (1.38) over (1.37+nmu1ubuntu1) ... 126s Preparing to unpack .../072-psmisc_23.7-2_armhf.deb ... 126s Unpacking psmisc (23.7-2) over (23.7-1build1) ... 126s Preparing to unpack .../073-publicsuffix_20250108.1153-0.1_all.deb ... 126s Unpacking publicsuffix (20250108.1153-0.1) over (20231001.0357-0.1) ... 126s Preparing to unpack .../074-python3-distro-info_1.13_all.deb ... 126s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 126s for fn in glob1(directory, "%s.*" % fname): 126s Unpacking python3-distro-info (1.13) over (1.12) ... 126s Preparing to unpack .../075-python3.13-gdbm_3.13.2-1_armhf.deb ... 126s Unpacking python3.13-gdbm (3.13.2-1) over (3.13.0-2) ... 126s Preparing to unpack .../076-python3.12-gdbm_3.12.9-1_armhf.deb ... 126s Unpacking python3.12-gdbm (3.12.9-1) over (3.12.7-3) ... 126s Preparing to unpack .../077-python3-gdbm_3.13.1-1_armhf.deb ... 126s Unpacking python3-gdbm:armhf (3.13.1-1) over (3.12.7-1) ... 126s Preparing to unpack .../078-ubuntu-standard_1.547_armhf.deb ... 126s Unpacking ubuntu-standard (1.547) over (1.544) ... 126s Preparing to unpack .../079-ufw_0.36.2-9_all.deb ... 126s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 126s for fn in glob1(directory, "%s.*" % fname): 126s Unpacking ufw (0.36.2-9) over (0.36.2-8) ... 126s Preparing to unpack .../080-usb.ids_2025.01.14-1_all.deb ... 126s Unpacking usb.ids (2025.01.14-1) over (2024.07.04-1) ... 126s Preparing to unpack .../081-xauth_1%3a1.1.2-1.1_armhf.deb ... 126s Unpacking xauth (1:1.1.2-1.1) over (1:1.1.2-1build1) ... 126s Preparing to unpack .../082-libcurl3t64-gnutls_8.12.0+git20250209.89ed161+ds-1ubuntu1_armhf.deb ... 126s Unpacking libcurl3t64-gnutls:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) over (8.11.0-1ubuntu2) ... 127s Preparing to unpack .../083-libappstream5_1.0.4-1_armhf.deb ... 127s Unpacking libappstream5:armhf (1.0.4-1) over (1.0.3-1) ... 127s Preparing to unpack .../084-appstream_1.0.4-1_armhf.deb ... 127s Unpacking appstream (1.0.4-1) over (1.0.3-1) ... 127s Preparing to unpack .../085-libctf0_2.44-1ubuntu1_armhf.deb ... 127s Unpacking libctf0:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../086-libctf-nobfd0_2.44-1ubuntu1_armhf.deb ... 127s Unpacking libctf-nobfd0:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../087-binutils-arm-linux-gnueabihf_2.44-1ubuntu1_armhf.deb ... 127s Unpacking binutils-arm-linux-gnueabihf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../088-libbinutils_2.44-1ubuntu1_armhf.deb ... 127s Unpacking libbinutils:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../089-binutils_2.44-1ubuntu1_armhf.deb ... 127s Unpacking binutils (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../090-binutils-common_2.44-1ubuntu1_armhf.deb ... 127s Unpacking binutils-common:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../091-libsframe1_2.44-1ubuntu1_armhf.deb ... 127s Unpacking libsframe1:armhf (2.44-1ubuntu1) over (2.43.1-4ubuntu1) ... 127s Preparing to unpack .../092-btrfs-progs_6.12-1build1_armhf.deb ... 127s Unpacking btrfs-progs (6.12-1build1) over (6.6.3-1.2) ... 127s Preparing to unpack .../093-python3-jinja2_3.1.5-2_all.deb ... 127s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 127s for fn in glob1(directory, "%s.*" % fname): 127s Unpacking python3-jinja2 (3.1.5-2) over (3.1.3-1ubuntu1) ... 127s Preparing to unpack .../094-python3-json-pointer_2.4-3_all.deb ... 127s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 127s for fn in glob1(directory, "%s.*" % fname): 127s Unpacking python3-json-pointer (2.4-3) over (2.4-2) ... 127s Preparing to unpack .../095-python3-jsonpatch_1.32-5_all.deb ... 127s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 127s for fn in glob1(directory, "%s.*" % fname): 127s Unpacking python3-jsonpatch (1.32-5) over (1.32-4) ... 127s Preparing to unpack .../096-python3-attr_25.1.0-1_all.deb ... 127s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 127s for fn in glob1(directory, "%s.*" % fname): 127s Unpacking python3-attr (25.1.0-1) over (23.2.0-2) ... 128s Preparing to unpack .../097-python3-referencing_0.35.1-2ubuntu1_all.deb ... 128s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 128s for fn in glob1(directory, "%s.*" % fname): 128s Unpacking python3-referencing (0.35.1-2ubuntu1) over (0.35.1-1ubuntu1) ... 128s Preparing to unpack .../098-python3-jsonschema_4.19.2-6ubuntu1_all.deb ... 128s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 128s for fn in glob1(directory, "%s.*" % fname): 128s Unpacking python3-jsonschema (4.19.2-6ubuntu1) over (4.19.2-3ubuntu1) ... 128s Preparing to unpack .../099-python3-jwt_2.10.1-2_all.deb ... 128s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 128s for fn in glob1(directory, "%s.*" % fname): 128s Unpacking python3-jwt (2.10.1-2) over (2.7.0-1) ... 128s Preparing to unpack .../100-python3-oauthlib_3.2.2-3_all.deb ... 128s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 128s for fn in glob1(directory, "%s.*" % fname): 128s Unpacking python3-oauthlib (3.2.2-3) over (3.2.2-2) ... 128s Preparing to unpack .../101-cloud-init-base_25.1~3geb1965a4-0ubuntu1_all.deb ... 128s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 128s for fn in glob1(directory, "%s.*" % fname): 128s Unpacking cloud-init-base (25.1~3geb1965a4-0ubuntu1) over (24.4-0ubuntu1) ... 128s dpkg: warning: unable to delete old directory '/lib/systemd/system/sshd-keygen@.service.d': Directory not empty 128s Preparing to unpack .../102-curl_8.12.0+git20250209.89ed161+ds-1ubuntu1_armhf.deb ... 128s Unpacking curl (8.12.0+git20250209.89ed161+ds-1ubuntu1) over (8.11.0-1ubuntu2) ... 128s Preparing to unpack .../103-libcurl4t64_8.12.0+git20250209.89ed161+ds-1ubuntu1_armhf.deb ... 128s Unpacking libcurl4t64:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) over (8.11.0-1ubuntu2) ... 129s Preparing to unpack .../104-dpkg-dev_1.22.11ubuntu4_all.deb ... 129s Unpacking dpkg-dev (1.22.11ubuntu4) over (1.22.11ubuntu3) ... 129s Preparing to unpack .../105-libdpkg-perl_1.22.11ubuntu4_all.deb ... 129s Unpacking libdpkg-perl (1.22.11ubuntu4) over (1.22.11ubuntu3) ... 129s Preparing to unpack .../106-make_4.4.1-1_armhf.deb ... 129s Unpacking make (4.4.1-1) over (4.3-4.1build2) ... 129s Preparing to unpack .../107-libarchive13t64_3.7.7-0ubuntu1_armhf.deb ... 129s Unpacking libarchive13t64:armhf (3.7.7-0ubuntu1) over (3.7.4-1.1) ... 129s Preparing to unpack .../108-libjson-glib-1.0-common_1.10.6+ds-1_all.deb ... 129s Unpacking libjson-glib-1.0-common (1.10.6+ds-1) over (1.10.0+ds-3) ... 129s Preparing to unpack .../109-libjson-glib-1.0-0_1.10.6+ds-1_armhf.deb ... 129s Unpacking libjson-glib-1.0-0:armhf (1.10.6+ds-1) over (1.10.0+ds-3) ... 129s Preparing to unpack .../110-fwupd_2.0.5-1_armhf.deb ... 129s Unpacking fwupd (2.0.5-1) over (2.0.2-1) ... 129s Preparing to unpack .../111-libfwupd3_2.0.5-1_armhf.deb ... 129s Unpacking libfwupd3:armhf (2.0.5-1) over (2.0.2-1) ... 129s Preparing to unpack .../112-polkitd_126-2_armhf.deb ... 129s Unpacking polkitd (126-2) over (125-2ubuntu1) ... 129s Preparing to unpack .../113-libpolkit-agent-1-0_126-2_armhf.deb ... 129s Unpacking libpolkit-agent-1-0:armhf (126-2) over (125-2ubuntu1) ... 129s Preparing to unpack .../114-libpolkit-gobject-1-0_126-2_armhf.deb ... 129s Unpacking libpolkit-gobject-1-0:armhf (126-2) over (125-2ubuntu1) ... 130s Preparing to unpack .../115-libprotobuf-c1_1.5.1-1ubuntu1_armhf.deb ... 130s Unpacking libprotobuf-c1:armhf (1.5.1-1ubuntu1) over (1.4.1-1ubuntu4) ... 130s Preparing to unpack .../116-libqmi-proxy_1.35.6-1_armhf.deb ... 130s Unpacking libqmi-proxy (1.35.6-1) over (1.35.2-0ubuntu2) ... 130s Preparing to unpack .../117-libqmi-glib5_1.35.6-1_armhf.deb ... 130s Unpacking libqmi-glib5:armhf (1.35.6-1) over (1.35.2-0ubuntu2) ... 130s Preparing to unpack .../118-libpackagekit-glib2-18_1.3.0-3build1_armhf.deb ... 130s Unpacking libpackagekit-glib2-18:armhf (1.3.0-3build1) over (1.3.0-2) ... 130s Preparing to unpack .../119-gir1.2-packagekitglib-1.0_1.3.0-3build1_armhf.deb ... 130s Unpacking gir1.2-packagekitglib-1.0 (1.3.0-3build1) over (1.3.0-2) ... 130s Preparing to unpack .../120-gnupg-l10n_2.4.4-2ubuntu22_all.deb ... 130s Unpacking gnupg-l10n (2.4.4-2ubuntu22) over (2.4.4-2ubuntu18) ... 130s Preparing to unpack .../121-htop_3.3.0-5_armhf.deb ... 130s Unpacking htop (3.3.0-5) over (3.3.0-4build1) ... 130s Preparing to unpack .../122-libblockdev-utils3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-utils3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../123-libnspr4_2%3a4.36-1ubuntu1_armhf.deb ... 130s Unpacking libnspr4:armhf (2:4.36-1ubuntu1) over (2:4.35-1.1ubuntu2) ... 130s Preparing to unpack .../124-libnss3_2%3a3.107-1ubuntu1_armhf.deb ... 130s Unpacking libnss3:armhf (2:3.107-1ubuntu1) over (2:3.103-1) ... 130s Preparing to unpack .../125-libgpgme11t64_1.24.1-4ubuntu1_armhf.deb ... 130s Unpacking libgpgme11t64:armhf (1.24.1-4ubuntu1) over (1.24.0-2ubuntu1) ... 130s Preparing to unpack .../126-libvolume-key1_0.3.12-9_armhf.deb ... 130s Unpacking libvolume-key1:armhf (0.3.12-9) over (0.3.12-8) ... 130s Preparing to unpack .../127-libblockdev-crypto3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-crypto3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../128-libblockdev-fs3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-fs3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../129-libblockdev-loop3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-loop3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../130-libblockdev-mdraid3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-mdraid3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../131-libnvme1t64_1.11.1-2_armhf.deb ... 130s Unpacking libnvme1t64 (1.11.1-2) over (1.11.1-1) ... 130s Preparing to unpack .../132-libblockdev-nvme3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-nvme3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../133-libblockdev-part3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-part3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../134-libblockdev-swap3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev-swap3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../135-libblockdev3_3.3.0-1_armhf.deb ... 130s Unpacking libblockdev3:armhf (3.3.0-1) over (3.2.1-1) ... 130s Preparing to unpack .../136-libftdi1-2_1.5-8_armhf.deb ... 130s Unpacking libftdi1-2:armhf (1.5-8) over (1.5-7build1) ... 130s Preparing to unpack .../137-libgstreamer1.0-0_1.25.50-1_armhf.deb ... 130s Unpacking libgstreamer1.0-0:armhf (1.25.50-1) over (1.24.9-1) ... 130s Preparing to unpack .../138-libgudev-1.0-0_1%3a238-6_armhf.deb ... 130s Unpacking libgudev-1.0-0:armhf (1:238-6) over (1:238-5ubuntu1) ... 130s Selecting previously unselected package libicu76:armhf. 130s Preparing to unpack .../139-libicu76_76.1-1ubuntu2_armhf.deb ... 130s Unpacking libicu76:armhf (76.1-1ubuntu2) ... 131s Preparing to unpack .../140-libsasl2-modules_2.1.28+dfsg1-8build1_armhf.deb ... 131s Unpacking libsasl2-modules:armhf (2.1.28+dfsg1-8build1) over (2.1.28+dfsg1-8) ... 131s Preparing to unpack .../141-udisks2_2.10.1-11ubuntu2_armhf.deb ... 131s Unpacking udisks2 (2.10.1-11ubuntu2) over (2.10.1-11ubuntu1) ... 131s Preparing to unpack .../142-libudisks2-0_2.10.1-11ubuntu2_armhf.deb ... 131s Unpacking libudisks2-0:armhf (2.10.1-11ubuntu2) over (2.10.1-11ubuntu1) ... 131s Preparing to unpack .../143-libwrap0_7.6.q-35_armhf.deb ... 131s Unpacking libwrap0:armhf (7.6.q-35) over (7.6.q-33) ... 131s Selecting previously unselected package linux-headers-6.12.0-15. 131s Preparing to unpack .../144-linux-headers-6.12.0-15_6.12.0-15.15_all.deb ... 131s Unpacking linux-headers-6.12.0-15 (6.12.0-15.15) ... 134s Selecting previously unselected package linux-headers-6.12.0-15-generic. 134s Preparing to unpack .../145-linux-headers-6.12.0-15-generic_6.12.0-15.15_armhf.deb ... 134s Unpacking linux-headers-6.12.0-15-generic (6.12.0-15.15) ... 135s Preparing to unpack .../146-linux-headers-generic_6.12.0-15.15+1_armhf.deb ... 135s Unpacking linux-headers-generic (6.12.0-15.15+1) over (6.11.0-8.8) ... 135s Preparing to unpack .../147-packagekit-tools_1.3.0-3build1_armhf.deb ... 135s Unpacking packagekit-tools (1.3.0-3build1) over (1.3.0-2) ... 135s Preparing to unpack .../148-packagekit_1.3.0-3build1_armhf.deb ... 135s Unpacking packagekit (1.3.0-3build1) over (1.3.0-2) ... 135s Preparing to unpack .../149-pollinate_4.33-4ubuntu2_all.deb ... 135s Unpacking pollinate (4.33-4ubuntu2) over (4.33-4ubuntu1) ... 135s Preparing to unpack .../150-python3-babel_2.17.0-1_all.deb ... 135s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 135s for fn in glob1(directory, "%s.*" % fname): 135s Unpacking python3-babel (2.17.0-1) over (2.16.0-1) ... 135s Preparing to unpack .../151-python-babel-localedata_2.17.0-1_all.deb ... 135s Unpacking python-babel-localedata (2.17.0-1) over (2.16.0-1) ... 135s Preparing to unpack .../152-python3-certifi_2025.1.31+ds-1_all.deb ... 135s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 135s for fn in glob1(directory, "%s.*" % fname): 135s Unpacking python3-certifi (2025.1.31+ds-1) over (2024.8.30+dfsg-1) ... 135s Preparing to unpack .../153-python3-chardet_5.2.0+dfsg-2_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking python3-chardet (5.2.0+dfsg-2) over (5.2.0+dfsg-1) ... 136s Preparing to unpack .../154-python3-idna_3.10-1_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking python3-idna (3.10-1) over (3.8-2) ... 136s Preparing to unpack .../155-python3-more-itertools_10.6.0-1_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking python3-more-itertools (10.6.0-1) over (10.5.0-1) ... 136s Preparing to unpack .../156-python3-openssl_25.0.0-1_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking python3-openssl (25.0.0-1) over (24.2.1-1) ... 136s Preparing to unpack .../157-python3-pkg-resources_75.6.0-1_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking python3-pkg-resources (75.6.0-1) over (75.2.0-1) ... 136s Preparing to unpack .../158-python3-setuptools_75.6.0-1_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking python3-setuptools (75.6.0-1) over (75.2.0-1) ... 136s Preparing to unpack .../159-software-properties-common_0.108_all.deb ... 136s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 136s for fn in glob1(directory, "%s.*" % fname): 136s Unpacking software-properties-common (0.108) over (0.105) ... 137s Preparing to unpack .../160-python3-software-properties_0.108_all.deb ... 137s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 137s for fn in glob1(directory, "%s.*" % fname): 137s Unpacking python3-software-properties (0.108) over (0.105) ... 137s Preparing to unpack .../161-python3-urllib3_2.3.0-1_all.deb ... 137s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 137s for fn in glob1(directory, "%s.*" % fname): 137s Unpacking python3-urllib3 (2.3.0-1) over (2.0.7-2ubuntu0.1) ... 137s Preparing to unpack .../162-python3-wadllib_2.0.0-2_all.deb ... 137s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 137s for fn in glob1(directory, "%s.*" % fname): 137s Unpacking python3-wadllib (2.0.0-2) over (2.0.0-1) ... 137s Preparing to unpack .../163-unattended-upgrades_2.12ubuntu2_all.deb ... 137s Unpacking unattended-upgrades (2.12ubuntu2) over (2.9.1+nmu4ubuntu1) ... 137s dpkg: warning: unable to delete old directory '/lib/systemd/system-sleep': Directory not empty 137s Preparing to unpack .../164-xfsprogs_6.12.0-1ubuntu1_armhf.deb ... 137s Unpacking xfsprogs (6.12.0-1ubuntu1) over (6.8.0-2.2ubuntu2) ... 137s Preparing to unpack .../165-zstd_1.5.6+dfsg-2_armhf.deb ... 137s Unpacking zstd (1.5.6+dfsg-2) over (1.5.6+dfsg-1) ... 137s Preparing to unpack .../166-cloud-init_25.1~3geb1965a4-0ubuntu1_all.deb ... 137s Unpacking cloud-init (25.1~3geb1965a4-0ubuntu1) over (24.4-0ubuntu1) ... 137s Preparing to unpack .../167-kpartx_0.9.9-1ubuntu4_armhf.deb ... 137s Unpacking kpartx (0.9.9-1ubuntu4) over (0.9.9-1ubuntu3) ... 137s Preparing to unpack .../168-multipath-tools_0.9.9-1ubuntu4_armhf.deb ... 137s Unpacking multipath-tools (0.9.9-1ubuntu4) over (0.9.9-1ubuntu3) ... 137s Setting up libip4tc2:armhf (1.8.11-2ubuntu1) ... 137s Setting up powermgmt-base (1.38) ... 137s Setting up distro-info (1.13) ... 137s Setting up liburcu8t64:armhf (0.15.0-1) ... 137s Setting up libibverbs1:armhf (55.0-1ubuntu1) ... 137s Setting up libxdmcp6:armhf (1:1.1.5-1) ... 137s Setting up pci.ids (0.0~2025.02.12-1) ... 137s Setting up libnewt0.52:armhf (0.52.24-4ubuntu1) ... 137s Setting up apt-utils (2.9.30) ... 137s Setting up bsdextrautils (2.40.2-14ubuntu1) ... 137s Setting up init (1.68) ... 137s Setting up ibverbs-providers:armhf (55.0-1ubuntu1) ... 137s Setting up gcc-14-base:armhf (14.2.0-17ubuntu1) ... 137s Setting up psmisc (23.7-2) ... 137s Setting up libyaml-0-2:armhf (0.2.5-2) ... 137s Setting up libip6tc2:armhf (1.8.11-2ubuntu1) ... 137s Setting up liblsof0 (4.99.4+dfsg-1) ... 137s Setting up libmaxminddb0:armhf (1.12.2-1) ... 137s Setting up python3.12-gdbm (3.12.9-1) ... 137s Setting up libedit2:armhf (3.1-20250104-1) ... 137s Setting up libsasl2-modules:armhf (2.1.28+dfsg1-8build1) ... 137s Setting up netcat-openbsd (1.228-1) ... 137s Setting up libpython3.12-minimal:armhf (3.12.9-1) ... 137s Setting up binutils-common:armhf (2.44-1ubuntu1) ... 137s Setting up libctf-nobfd0:armhf (2.44-1ubuntu1) ... 137s Setting up gettext-base (0.23.1-1) ... 137s Setting up libnss-systemd:armhf (257.2-3ubuntu1) ... 137s Setting up libnftnl11:armhf (1.2.8-1) ... 137s Setting up krb5-locales (1.21.3-4ubuntu1) ... 137s Setting up libcom-err2:armhf (1.47.2-1ubuntu1) ... 137s Setting up lshw (02.19.git.2021.06.19.996aaad9c7-2.1ubuntu1) ... 137s Setting up locales (2.40-4ubuntu1) ... 138s Generating locales (this might take a while)... 140s en_US.UTF-8... done 140s Generation complete. 140s Setting up libldap-common (2.6.9+dfsg-1~exp2ubuntu1) ... 140s Installing new version of config file /etc/ldap/ldap.conf ... 140s Setting up libprotobuf-c1:armhf (1.5.1-1ubuntu1) ... 140s Setting up libsframe1:armhf (2.44-1ubuntu1) ... 140s Setting up python-babel-localedata (2.17.0-1) ... 140s Setting up libkrb5support0:armhf (1.21.3-4ubuntu1) ... 140s Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8build1) ... 140s Setting up tzdata (2025a-2ubuntu1) ... 140s 140s Current default time zone: 'Etc/UTC' 140s Local time is now: Wed Feb 19 12:04:51 UTC 2025. 140s Universal Time is now: Wed Feb 19 12:04:51 UTC 2025. 140s Run 'dpkg-reconfigure tzdata' if you wish to change it. 140s 140s Setting up eject (2.40.2-14ubuntu1) ... 140s Setting up apparmor (4.1.0~beta1-0ubuntu5) ... 140s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 140s 140s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 140s 140s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 140s 141s Reloading AppArmor profiles 141s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "busybox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "nautilus". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "toybox". /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 141s 141s Error: At least one profile failed to load 141s Setting up libglib2.0-data (2.83.3-2) ... 141s Setting up busybox-static (1:1.37.0-4ubuntu1) ... 141s Setting up systemd-cryptsetup (257.2-3ubuntu1) ... 141s Setting up libwrap0:armhf (7.6.q-35) ... 141s Setting up libnvme1t64 (1.11.1-2) ... 141s Setting up make (4.4.1-1) ... 141s Setting up libnspr4:armhf (2:4.36-1ubuntu1) ... 141s Setting up gnupg-l10n (2.4.4-2ubuntu22) ... 141s Setting up ed (1.21-1) ... 141s Setting up bash-completion (1:2.16.0-7) ... 141s Setting up libncurses6:armhf (6.5+20250125-2) ... 141s Setting up libdbus-1-3:armhf (1.16.0-1ubuntu1) ... 141s Setting up libfribidi0:armhf (1.0.16-1) ... 141s Setting up libpng16-16t64:armhf (1.6.46-4) ... 141s Setting up systemd-timesyncd (257.2-3ubuntu1) ... 142s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 142s Setting up libatomic1:armhf (15-20250213-1ubuntu1) ... 142s Setting up udev (257.2-3ubuntu1) ... 143s Setting up libss2:armhf (1.47.2-1ubuntu1) ... 143s Setting up usb.ids (2025.01.14-1) ... 143s Setting up dhcpcd-base (1:10.1.0-7) ... 143s Installing new version of config file /etc/dhcpcd.conf ... 143s Setting up ucf (3.0049) ... 143s Installing new version of config file /etc/ucf.conf ... 143s Setting up libncursesw6:armhf (6.5+20250125-2) ... 143s Setting up libk5crypto3:armhf (1.21.3-4ubuntu1) ... 143s Setting up busybox-initramfs (1:1.37.0-4ubuntu1) ... 143s Setting up libxtables12:armhf (1.8.11-2ubuntu1) ... 143s Setting up libdpkg-perl (1.22.11ubuntu4) ... 143s Setting up logsave (1.47.2-1ubuntu1) ... 143s Setting up libsasl2-2:armhf (2.1.28+dfsg1-8build1) ... 143s Setting up lsof (4.99.4+dfsg-1) ... 143s Setting up libfdisk1:armhf (2.40.2-14ubuntu1) ... 143s Setting up libicu74:armhf (74.2-1ubuntu6) ... 143s Setting up nano (8.3-1) ... 143s Installing new version of config file /etc/nanorc ... 143s Setting up libdevmapper1.02.1:armhf (2:1.02.201-1ubuntu1) ... 143s Setting up whiptail (0.52.24-4ubuntu1) ... 143s Setting up python-apt-common (2.9.8) ... 143s Setting up dracut-install (106-2ubuntu1) ... 143s Setting up dmsetup (2:1.02.201-1ubuntu1) ... 143s Setting up uuid-runtime (2.40.2-14ubuntu1) ... 144s uuidd.service is a disabled or a static unit not running, not starting it. 144s Setting up xauth (1:1.1.2-1.1) ... 144s Setting up groff-base (1.23.0-7) ... 144s Setting up libtraceevent1:armhf (1:1.8.4-2) ... 144s Setting up dbus-session-bus-common (1.16.0-1ubuntu1) ... 144s Setting up kpartx (0.9.9-1ubuntu4) ... 144s Setting up libpcap0.8t64:armhf (1.10.5-2ubuntu1) ... 144s Setting up libjson-glib-1.0-common (1.10.6+ds-1) ... 144s Setting up mawk (1.3.4.20250131-1) ... 144s Setting up libkrb5-3:armhf (1.21.3-4ubuntu1) ... 144s Setting up libusb-1.0-0:armhf (2:1.0.27-2) ... 144s Setting up libicu76:armhf (76.1-1ubuntu2) ... 144s Setting up linux-headers-6.12.0-15 (6.12.0-15.15) ... 144s Setting up keyboard-configuration (1.226ubuntu3) ... 144s Your console font configuration will be updated the next time your system 144s boots. If you want to update it now, run 'setupcon' from a virtual console. 144s update-initramfs: deferring update (trigger activated) 144s Setting up libbinutils:armhf (2.44-1ubuntu1) ... 144s Setting up dbus-system-bus-common (1.16.0-1ubuntu1) ... 144s Setting up openssl (3.4.0-1ubuntu2) ... 144s Installing new version of config file /etc/ssl/openssl.cnf ... 144s Setting up libgpg-error-l10n (1.51-3) ... 144s Setting up iputils-ping (3:20240905-1ubuntu1) ... 145s Setting up readline-common (8.2-6) ... 145s Setting up publicsuffix (20250108.1153-0.1) ... 145s Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2ubuntu3) ... 145s Setting up zstd (1.5.6+dfsg-2) ... 145s Setting up libldap2:armhf (2.6.9+dfsg-1~exp2ubuntu1) ... 145s Setting up dbus-bin (1.16.0-1ubuntu1) ... 145s Setting up libbpf1:armhf (1:1.5.0-2) ... 145s Setting up iputils-tracepath (3:20240905-1ubuntu1) ... 145s Setting up rsync (3.4.1-0syncable1) ... 145s rsync.service is a disabled or a static unit not running, not starting it. 145s Setting up python3.13-gdbm (3.13.2-1) ... 145s Setting up ethtool (1:6.11-1) ... 145s Setting up gnupg-utils (2.4.4-2ubuntu22) ... 145s Setting up initramfs-tools-bin (0.145ubuntu2) ... 145s Setting up ncurses-term (6.5+20250125-2) ... 145s Setting up login (1:4.16.0-2+really2.40.2-14ubuntu1) ... 145s Setting up cron-daemon-common (3.0pl1-192ubuntu1) ... 145s Setting up libxkbcommon0:armhf (1.7.0-2) ... 145s Setting up libctf0:armhf (2.44-1ubuntu1) ... 145s Setting up pinentry-curses (1.3.1-2ubuntu2) ... 145s Setting up python3.12-minimal (3.12.9-1) ... 146s Setting up libnftables1:armhf (1.1.1-1build1) ... 146s Setting up nftables (1.1.1-1build1) ... 147s Setting up iptables (1.8.11-2ubuntu1) ... 147s Setting up htop (3.3.0-5) ... 147s Setting up iproute2 (6.13.0-1ubuntu1) ... 147s Setting up btrfs-progs (6.12-1build1) ... 147s Setting up cron (3.0pl1-192ubuntu1) ... 147s Setting up rsyslog (8.2412.0-2ubuntu1) ... 147s Installing new version of config file /etc/apparmor.d/usr.sbin.rsyslogd ... 147s info: The user `syslog' is already a member of `adm'. 148s apparmor_parser: Unable to replace "rsyslogd". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 148s 148s Setting up e2fsprogs (1.47.2-1ubuntu1) ... 148s update-initramfs: deferring update (trigger activated) 149s Setting up libnss3:armhf (2:3.107-1ubuntu1) ... 149s Setting up dbus-daemon (1.16.0-1ubuntu1) ... 149s Setting up multipath-tools (0.9.9-1ubuntu4) ... 149s Setting up libftdi1-2:armhf (1.5-8) ... 149s Setting up ca-certificates (20241223) ... 152s Updating certificates in /etc/ssl/certs... 153s rehash: warning: skipping ca-certificates.crt, it does not contain exactly one certificate or CRL 153s 7 added, 1 removed; done. 153s Setting up libglib2.0-0t64:armhf (2.83.3-2) ... 153s No schema files found: doing nothing. 153s Setting up dbus (1.16.0-1ubuntu1) ... 153s A reboot is required to replace the running dbus-daemon. 153s Please reboot the system when convenient. 153s Setting up libblockdev-utils3:armhf (3.3.0-1) ... 153s Setting up linux-headers-6.12.0-15-generic (6.12.0-15.15) ... 153s Setting up libgssapi-krb5-2:armhf (1.21.3-4ubuntu1) ... 153s Setting up gir1.2-glib-2.0:armhf (2.83.3-2) ... 153s Setting up libreadline8t64:armhf (8.2-6) ... 153s Setting up libblockdev-nvme3:armhf (3.3.0-1) ... 153s Setting up libblockdev-fs3:armhf (3.3.0-1) ... 153s Setting up libtraceevent1-plugin:armhf (1:1.8.4-2) ... 153s Setting up gpgconf (2.4.4-2ubuntu22) ... 153s Setting up libpam-systemd:armhf (257.2-3ubuntu1) ... 153s Setting up libgirepository-1.0-1:armhf (1.82.0-4) ... 153s Setting up console-setup-linux (1.226ubuntu3) ... 154s Setting up initramfs-tools-core (0.145ubuntu2) ... 154s Setting up binutils-arm-linux-gnueabihf (2.44-1ubuntu1) ... 154s Setting up libarchive13t64:armhf (3.7.7-0ubuntu1) ... 154s Setting up libpython3.13-stdlib:armhf (3.13.2-1) ... 154s Setting up gpg (2.4.4-2ubuntu22) ... 154s Setting up libgudev-1.0-0:armhf (1:238-6) ... 154s Setting up libpolkit-gobject-1-0:armhf (126-2) ... 154s Setting up libgstreamer1.0-0:armhf (1.25.50-1) ... 154s Setcap worked! gst-ptp-helper is not suid! 154s Setting up libudisks2-0:armhf (2.10.1-11ubuntu2) ... 154s Setting up libpython3-stdlib:armhf (3.13.1-1~exp2) ... 154s Setting up systemd-resolved (257.2-3ubuntu1) ... 155s Setting up console-setup (1.226ubuntu3) ... 156s update-initramfs: deferring update (trigger activated) 156s Setting up gpg-agent (2.4.4-2ubuntu22) ... 156s Setting up libpython3.12-stdlib:armhf (3.12.9-1) ... 156s Setting up initramfs-tools (0.145ubuntu2) ... 156s update-initramfs: deferring update (trigger activated) 156s Setting up libblockdev-mdraid3:armhf (3.3.0-1) ... 156s Setting up libcurl4t64:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) ... 156s Setting up bind9-libs:armhf (1:9.20.0-2ubuntu4) ... 156s Setting up e2fsprogs-l10n (1.47.2-1ubuntu1) ... 156s Setting up python3.13 (3.13.2-1) ... 157s Setting up libblockdev-swap3:armhf (3.3.0-1) ... 157s Setting up python3.12 (3.12.9-1) ... 158s Setting up libblockdev-loop3:armhf (3.3.0-1) ... 158s Setting up gpgsm (2.4.4-2ubuntu22) ... 158s Setting up libcurl3t64-gnutls:armhf (8.12.0+git20250209.89ed161+ds-1ubuntu1) ... 158s Setting up libglib2.0-bin (2.83.3-2) ... 158s Setting up libpackagekit-glib2-18:armhf (1.3.0-3build1) ... 158s Setting up libappstream5:armhf (1.0.4-1) ... 158s Setting up libqmi-glib5:armhf (1.35.6-1) ... 158s Setting up python3 (3.13.1-1~exp2) ... 158s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 158s for fn in glob1(directory, "%s.*" % fname): 158s Setting up linux-headers-generic (6.12.0-15.15+1) ... 158s Setting up binutils (2.44-1ubuntu1) ... 158s Setting up libnetplan1:armhf (1.1.2-2ubuntu1) ... 158s Setting up python3-newt:armhf (0.52.24-4ubuntu1) ... 159s Setting up libblockdev3:armhf (3.3.0-1) ... 159s Setting up fdisk (2.40.2-14ubuntu1) ... 159s Setting up dpkg-dev (1.22.11ubuntu4) ... 159s Setting up libjson-glib-1.0-0:armhf (1.10.6+ds-1) ... 159s Setting up libblockdev-part3:armhf (3.3.0-1) ... 159s Setting up dirmngr (2.4.4-2ubuntu22) ... 159s Setting up gir1.2-packagekitglib-1.0 (1.3.0-3build1) ... 159s Setting up dbus-user-session (1.16.0-1ubuntu1) ... 159s Setting up python3-jinja2 (3.1.5-2) ... 159s Setting up python3-pygments (2.18.0+dfsg-2) ... 161s Setting up python3-chardet (5.2.0+dfsg-2) ... 161s Setting up appstream (1.0.4-1) ... 163s ✔ Metadata cache was updated successfully. 163s Setting up python3-certifi (2025.1.31+ds-1) ... 163s Setting up gir1.2-girepository-2.0:armhf (1.82.0-4) ... 163s Setting up python3-gi (3.50.0-4) ... 164s Setting up python3-idna (3.10-1) ... 164s Setting up xfsprogs (6.12.0-1ubuntu1) ... 164s update-initramfs: deferring update (trigger activated) 165s Setting up keyboxd (2.4.4-2ubuntu22) ... 165s Setting up python3-urllib3 (2.3.0-1) ... 165s Setting up python3-json-pointer (2.4-3) ... 165s Setting up gnupg (2.4.4-2ubuntu22) ... 165s Setting up python3-netplan (1.1.2-2ubuntu1) ... 165s Setting up libpolkit-agent-1-0:armhf (126-2) ... 165s Setting up libgpgme11t64:armhf (1.24.1-4ubuntu1) ... 165s Setting up curl (8.12.0+git20250209.89ed161+ds-1ubuntu1) ... 165s Setting up libvolume-key1:armhf (0.3.12-9) ... 165s Setting up netplan-generator (1.1.2-2ubuntu1) ... 165s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 165s Setting up bind9-host (1:9.20.0-2ubuntu4) ... 165s Setting up python3-distro-info (1.13) ... 165s Setting up polkitd (126-2) ... 166s Setting up python3-more-itertools (10.6.0-1) ... 166s Setting up python3-attr (25.1.0-1) ... 166s Setting up gpg-wks-client (2.4.4-2ubuntu22) ... 166s Setting up libblockdev-crypto3:armhf (3.3.0-1) ... 166s Setting up python3-jwt (2.10.1-2) ... 167s Setting up python3-babel (2.17.0-1) ... 167s Setting up python3-rich (13.9.4-1) ... 168s Setting up python3-gdbm:armhf (3.13.1-1) ... 168s Setting up python3-problem-report (2.31.0-0ubuntu5) ... 168s Setting up python3-apt (2.9.8) ... 168s Setting up python3-jsonpatch (1.32-5) ... 168s Setting up python3-bcrypt (4.2.0-2.1) ... 169s Setting up libqmi-proxy (1.35.6-1) ... 169s Setting up libfwupd3:armhf (2.0.5-1) ... 169s Setting up ufw (0.36.2-9) ... 170s Setting up python3-lazr.uri (1.0.6-5) ... 170s Setting up netplan.io (1.1.2-2ubuntu1) ... 170s Setting up unattended-upgrades (2.12ubuntu2) ... 170s Replacing config file /etc/apt/apt.conf.d/50unattended-upgrades with new version 171s Setting up pollinate (4.33-4ubuntu2) ... 171s Setting up python3-cryptography (43.0.0-1) ... 172s Setting up python3-wadllib (2.0.0-2) ... 172s Setting up bind9-dnsutils (1:9.20.0-2ubuntu4) ... 172s Setting up fwupd (2.0.5-1) ... 173s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 173s fwupd.service is a disabled or a static unit not running, not starting it. 173s Setting up python3-referencing (0.35.1-2ubuntu1) ... 173s Setting up python3-pkg-resources (75.6.0-1) ... 173s Setting up udisks2 (2.10.1-11ubuntu2) ... 173s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 173s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 173s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 173s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 173s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 173s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 173s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 173s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 173s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 173s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 173s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 173s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 173s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied 174s Setting up python3-setuptools (75.6.0-1) ... 176s Setting up ubuntu-minimal (1.547) ... 176s Setting up python3-openssl (25.0.0-1) ... 176s Setting up python3-launchpadlib (2.1.0-1) ... 176s Setting up ubuntu-standard (1.547) ... 176s Setting up python3-apport (2.31.0-0ubuntu5) ... 176s Setting up python3-oauthlib (3.2.2-3) ... 177s Setting up python3-software-properties (0.108) ... 177s Setting up python3-jsonschema (4.19.2-6ubuntu1) ... 177s Setting up cloud-init-base (25.1~3geb1965a4-0ubuntu1) ... 177s Installing new version of config file /etc/cloud/templates/sources.list.debian.deb822.tmpl ... 177s Installing new version of config file /etc/cloud/templates/sources.list.ubuntu.deb822.tmpl ... 179s Setting up cloud-init (25.1~3geb1965a4-0ubuntu1) ... 179s Setting up apport-core-dump-handler (2.31.0-0ubuntu5) ... 180s Setting up apport (2.31.0-0ubuntu5) ... 181s apport-autoreport.service is a disabled or a static unit not running, not starting it. 181s Processing triggers for shared-mime-info (2.4-5) ... 181s Warning: program compiled against libxml 212 using older 209 181s Processing triggers for sgml-base (1.31) ... 181s Processing triggers for debianutils (5.21) ... 181s Processing triggers for install-info (7.1.1-1) ... 182s Processing triggers for libc-bin (2.40-4ubuntu1) ... 182s Processing triggers for systemd (257.2-3ubuntu1) ... 182s Processing triggers for man-db (2.13.0-1) ... 183s Setting up packagekit (1.3.0-3build1) ... 183s Setting up packagekit-tools (1.3.0-3build1) ... 183s Setting up software-properties-common (0.108) ... 183s Processing triggers for ca-certificates (20241223) ... 183s Updating certificates in /etc/ssl/certs... 184s 0 added, 0 removed; done. 184s Running hooks in /etc/ca-certificates/update.d... 184s done. 184s Processing triggers for initramfs-tools (0.145ubuntu2) ... 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s The following packages will be REMOVED: 190s libassuan0* libicu74* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 190s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 190s python3.12* python3.12-minimal* 190s 0 upgraded, 0 newly installed, 10 to remove and 0 not upgraded. 190s After this operation, 151 MB disk space will be freed. 190s (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 ... 92763 files and directories currently installed.) 190s Removing libassuan0:armhf (2.5.6-1build1) ... 190s Removing libicu74:armhf (74.2-1ubuntu6) ... 190s Removing python3.12 (3.12.9-1) ... 190s Removing libpython3.12-stdlib:armhf (3.12.9-1) ... 190s Removing libnsl2:armhf (1.3.0-3build3) ... 190s Removing python3.12-minimal (3.12.9-1) ... 190s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 190s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 191s Removing libpython3.12-minimal:armhf (3.12.9-1) ... 191s Removing libunwind8:armhf (1.6.2-3.1) ... 191s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 191s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 192s Processing triggers for systemd (257.2-3ubuntu1) ... 192s Processing triggers for man-db (2.13.0-1) ... 193s Processing triggers for libc-bin (2.40-4ubuntu1) ... 193s (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 ... 60307 files and directories currently installed.) 193s Purging configuration files for python3.12-minimal (3.12.9-1) ... 193s Purging configuration files for libpython3.12-minimal:armhf (3.12.9-1) ... 196s autopkgtest [12:05:47]: rebooting testbed after setup commands that affected boot 245s autopkgtest [12:06:36]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 277s autopkgtest [12:07:08]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 296s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.8.0-2 (dsc) [2952 B] 296s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.8.0-2 (tar) [60.8 MB] 296s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.8.0-2 (diff) [11.1 kB] 296s gpgv: Signature made Fri Feb 14 13:13:06 2025 UTC 296s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 296s gpgv: issuer "dparsons@debian.org" 296s gpgv: Can't check signature: No public key 296s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.8.0-2.dsc: no acceptable signature found 298s autopkgtest [12:07:29]: testing package mdanalysis version 2.8.0-2 300s autopkgtest [12:07:31]: build not needed 309s autopkgtest [12:07:40]: test test-mdanalysis: preparing testbed 311s Reading package lists... 311s Building dependency tree... 311s Reading state information... 311s Starting pkgProblemResolver with broken count: 0 311s Starting 2 pkgProblemResolver with broken count: 0 311s Done 312s The following NEW packages will be installed: 312s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 312s cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper 312s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 312s dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 312s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 312s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 312s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 312s libaec0 libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev 312s libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl libdeflate0 libexpat1-dev 312s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6 312s libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-310 312s libhdf5-hl-310 libimagequant0 libisl23 libjbig0 libjpeg-turbo8 libjpeg8 312s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 312s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libmpc3 312s libnetcdf22 libnsl2 libopenjp2-7 libpixman-1-0 libpython3-all-dev 312s libpython3-dev libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib 312s libpython3.12t64 libpython3.13 libpython3.13-dev libqhull-r8.0 libraqm0 312s libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool 312s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 312s libxft2 libxrender1 libxslt1.1 libxss1 linux-libc-dev m4 po-debconf 312s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 312s python3-alabaster python3-all python3-all-dev python3-biopython 312s python3-brotli python3-build python3-cairo python3-cftime python3-citeproc 312s python3-contourpy python3-cycler python3-dateutil python3-decorator 312s python3-defusedxml python3-dev python3-docutils python3-duecredit 312s python3-fasteners python3-fonttools python3-freetype python3-fs 312s python3-griddataformats python3-gsd python3-h5py python3-h5py-serial 312s python3-hypothesis python3-imagesize python3-iniconfig python3-installer 312s python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion 312s python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib 312s python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath 312s python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4 312s python3-networkx python3-numpy python3-packaging python3-pandas 312s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 312s python3-pluggy python3-pybtex python3-pybtex-docutils 312s python3-pyproject-hooks python3-pytest python3-pytz python3-reportlab 312s python3-rlpycairo python3-roman python3-scipy python3-seaborn python3-six 312s python3-sklearn python3-sklearn-lib python3-snowballstemmer 312s python3-sortedcontainers python3-sphinx python3-sphinx-rtd-theme 312s python3-sphinx-sitemap python3-sphinxcontrib.bibtex 312s python3-sphinxcontrib.jquery python3-sympy python3-threadpoolctl python3-tk 312s python3-toml python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 312s python3-wheel python3.12 python3.12-dev python3.12-minimal python3.12-tk 312s python3.13-dev python3.13-tk rpcsvc-proto sphinx-common 312s sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 312s xfonts-encodings xfonts-utils zlib1g-dev 312s 0 upgraded, 212 newly installed, 0 to remove and 0 not upgraded. 312s Need to get 209 MB/215 MB of archives. 312s After this operation, 876 MB of additional disk space will be used. 312s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 313s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libnsl2 armhf 1.3.0-3build3 [36.5 kB] 313s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-5 [238 kB] 313s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 313s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 313s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.17-3 [572 kB] 313s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.23.1-1 [619 kB] 313s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 313s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 313s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 313s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 313s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 313s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 313s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 313s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 313s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 314s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 314s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 314s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 314s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 314s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 314s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 314s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB] 314s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B] 314s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-4ubuntu1 [19.2 kB] 314s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.12.0-15.15 [1697 kB] 314s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 314s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 314s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-4ubuntu1 [1358 kB] 314s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 314s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 314s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu1 [9220 kB] 314s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu1 [1034 B] 314s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 314s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 314s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250213-1ubuntu1 [38.9 kB] 314s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250213-1ubuntu1 [128 kB] 314s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250213-1ubuntu1 [2956 kB] 314s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250213-1ubuntu1 [1190 kB] 314s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu1 [897 kB] 314s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu1 [18.0 MB] 315s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu1 [506 kB] 315s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 315s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 315s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu1 [2573 kB] 315s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu1 [10.5 MB] 315s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu1 [21.8 kB] 315s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 315s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 315s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 315s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-2ubuntu1 [3062 kB] 315s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 315s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.5.4-3build1 [168 kB] 315s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 315s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 315s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 315s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.1-2 [5064 B] 315s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-2 [46.7 kB] 315s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 315s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.23.1-1 [1053 kB] 315s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 315s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 315s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.24.1ubuntu2 [895 kB] 315s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20250108 [117 kB] 315s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 315s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 315s Get:67 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.3-1 [171 kB] 315s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 315s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 315s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 315s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 315s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 315s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 315s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 315s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 315s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.4-1 [121 kB] 315s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250213-1ubuntu1 [330 kB] 315s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 315s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 315s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 315s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 315s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [58.8 kB] 315s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 315s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 315s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 315s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 315s Get:87 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 315s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 315s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 315s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB] 315s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 316s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 316s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 316s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 316s Get:95 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 316s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetcdf22 armhf 1:4.9.3-1 [459 kB] 316s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13 armhf 3.13.2-1 [2075 kB] 316s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 316s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-dev armhf 3.13.2-1 [4264 kB] 316s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.13.1-1~exp2 [10.5 kB] 316s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.9-1 [2077 kB] 316s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.9-1 [4345 kB] 317s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.13.1-1~exp2 [922 B] 317s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 317s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 317s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 317s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 317s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 317s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 317s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 317s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 317s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu2 [152 kB] 317s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.2-1 [51.5 kB] 317s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 317s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-toml all 0.10.2-1 [16.5 kB] 317s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-wheel all 0.45.1-1 [57.7 kB] 317s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-build all 1.2.2-1 [31.0 kB] 317s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 317s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf pybuild-plugin-pyproject all 6.20250108 [1726 B] 317s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 317s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 317s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf python-mdanalysis-doc all 2.8.0-2 [3459 kB] 317s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.1-1~exp2 [896 B] 317s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-dev armhf 3.13.2-1 [508 kB] 317s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.13.1-1~exp2 [26.7 kB] 317s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.9-1 [504 kB] 317s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.13.1-1~exp2 [918 B] 317s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-13 [3978 kB] 317s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.9-1 [113 kB] 317s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-tk armhf 3.13.2-1 [103 kB] 317s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.13.1-1 [9770 B] 317s Get:132 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 11.1.0-5 [9208 B] 317s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu3 [171 kB] 317s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 11.1.0-5 [453 kB] 317s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2build1 [129 kB] 317s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 317s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 317s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.3.0-1 [1137 kB] 317s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 317s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.85+dfsg-2 [1696 kB] 317s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build3 [324 kB] 317s Get:142 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cftime armhf 1.6.4-1build2 [304 kB] 317s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.1-1 [1631 kB] 317s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-citeproc all 0.6.0-3 [98.4 kB] 317s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.1-1 [240 kB] 317s Get:146 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 317s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 317s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 317s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-3 [42.2 kB] 317s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 5.0-1 [10.3 kB] 317s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 317s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-looseversion all 1.3.0-3 [8354 B] 318s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-duecredit all 0.10.2-2 [66.0 kB] 318s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf python3-monotonic all 1.6-3 [5344 B] 318s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf python3-fasteners all 0.18-2 [12.5 kB] 318s Get:156 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pytz all 2025.1-3 [162 kB] 318s Get:157 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2025.1-3 [1866 B] 318s Get:158 http://ftpmaster.internal/ubuntu plucky/main armhf python3-platformdirs all 4.3.6-1 [16.8 kB] 318s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-6 [90.7 kB] 318s Get:160 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.4.0+dfsg-1 [25.6 kB] 318s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu1 [19.5 MB] 318s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 318s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB] 318s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 318s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-unicodedata2 armhf 15.1.0+ds-1build2 [357 kB] 318s Get:166 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 319s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.55.3-2 [1625 kB] 319s Get:168 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 319s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mrcfile all 1.5.4-2 [116 kB] 319s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-griddataformats all 1.0.2-2 [2107 kB] 319s Get:171 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-gsd armhf 3.3.0-1build2 [225 kB] 319s Get:172 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.12.1-1 [1489 kB] 319s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.12.1-1 [7970 B] 319s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sortedcontainers all 2.4.0-2 [27.6 kB] 319s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-hypothesis all 6.125.2-1 [333 kB] 319s Get:176 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B] 319s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 319s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.4.2-2 [205 kB] 319s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-3 [70.4 kB] 319s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-latexcodec all 3.0.0-1 [16.6 kB] 319s Get:181 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3ubuntu2 [4598 kB] 319s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 319s Get:183 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build3 [106 kB] 319s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 319s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB] 319s Get:186 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.1-2 [92.5 kB] 319s Get:187 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mdanalysis armhf 2.8.0-2 [4319 kB] 320s Get:188 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf sphinx-common all 8.1.3-5 [663 kB] 320s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 320s Get:190 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 320s Get:191 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-sphinx all 8.1.3-5 [474 kB] 320s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 320s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 320s Get:194 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-msmb-theme all 1.2.0-4 [35.4 kB] 320s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-netcdf4 armhf 1.7.2-1build3 [848 kB] 320s Get:196 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 320s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-8 [7617 kB] 320s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-8 [3112 kB] 320s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 320s Get:200 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.17.0-1 [13.2 kB] 320s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex all 0.24.0-4 [70.0 kB] 320s Get:202 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex-docutils all 1.0.2-1 [7176 B] 321s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.4-1 [252 kB] 321s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-seaborn all 0.13.2-4.1 [225 kB] 321s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-7build1 [6341 kB] 322s Get:206 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 322s Get:207 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-sitemap all 2.6.0-1 [6674 B] 322s Get:208 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 322s Fetched 209 MB in 9s (22.4 MB/s) 322s Selecting previously unselected package libpython3.12-minimal:armhf. 322s (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 ... 60305 files and directories currently installed.) 322s Preparing to unpack .../000-libpython3.12-minimal_3.12.9-1_armhf.deb ... 322s Unpacking libpython3.12-minimal:armhf (3.12.9-1) ... 322s Selecting previously unselected package python3.12-minimal. 323s Preparing to unpack .../001-python3.12-minimal_3.12.9-1_armhf.deb ... 323s Unpacking python3.12-minimal (3.12.9-1) ... 323s Selecting previously unselected package fonts-lato. 323s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 323s Unpacking fonts-lato (2.015-1) ... 323s Selecting previously unselected package libnsl2:armhf. 323s Preparing to unpack .../003-libnsl2_1.3.0-3build3_armhf.deb ... 323s Unpacking libnsl2:armhf (1.3.0-3build3) ... 323s Selecting previously unselected package libpython3.12-stdlib:armhf. 323s Preparing to unpack .../004-libpython3.12-stdlib_3.12.9-1_armhf.deb ... 323s Unpacking libpython3.12-stdlib:armhf (3.12.9-1) ... 323s Selecting previously unselected package python3.12. 323s Preparing to unpack .../005-python3.12_3.12.9-1_armhf.deb ... 323s Unpacking python3.12 (3.12.9-1) ... 323s Selecting previously unselected package m4. 323s Preparing to unpack .../006-m4_1.4.19-5_armhf.deb ... 323s Unpacking m4 (1.4.19-5) ... 323s Selecting previously unselected package autoconf. 323s Preparing to unpack .../007-autoconf_2.72-3_all.deb ... 323s Unpacking autoconf (2.72-3) ... 323s Selecting previously unselected package autotools-dev. 323s Preparing to unpack .../008-autotools-dev_20220109.1_all.deb ... 323s Unpacking autotools-dev (20220109.1) ... 323s Selecting previously unselected package automake. 323s Preparing to unpack .../009-automake_1%3a1.17-3_all.deb ... 323s Unpacking automake (1:1.17-3) ... 323s Selecting previously unselected package autopoint. 323s Preparing to unpack .../010-autopoint_0.23.1-1_all.deb ... 323s Unpacking autopoint (0.23.1-1) ... 323s Selecting previously unselected package libtcl8.6:armhf. 323s Preparing to unpack .../011-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 323s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 323s Selecting previously unselected package libfreetype6:armhf. 323s Preparing to unpack .../012-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 323s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 323s Selecting previously unselected package fonts-dejavu-mono. 323s Preparing to unpack .../013-fonts-dejavu-mono_2.37-8_all.deb ... 323s Unpacking fonts-dejavu-mono (2.37-8) ... 323s Selecting previously unselected package fonts-dejavu-core. 323s Preparing to unpack .../014-fonts-dejavu-core_2.37-8_all.deb ... 323s Unpacking fonts-dejavu-core (2.37-8) ... 323s Selecting previously unselected package libfontenc1:armhf. 323s Preparing to unpack .../015-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 323s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 323s Selecting previously unselected package x11-common. 323s Preparing to unpack .../016-x11-common_1%3a7.7+23ubuntu3_all.deb ... 323s Unpacking x11-common (1:7.7+23ubuntu3) ... 323s Selecting previously unselected package xfonts-encodings. 323s Preparing to unpack .../017-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 323s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 323s Selecting previously unselected package xfonts-utils. 324s Preparing to unpack .../018-xfonts-utils_1%3a7.7+7_armhf.deb ... 324s Unpacking xfonts-utils (1:7.7+7) ... 324s Selecting previously unselected package fonts-urw-base35. 324s Preparing to unpack .../019-fonts-urw-base35_20200910-8_all.deb ... 324s Unpacking fonts-urw-base35 (20200910-8) ... 324s Selecting previously unselected package fontconfig-config. 324s Preparing to unpack .../020-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 324s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 324s Selecting previously unselected package libfontconfig1:armhf. 324s Preparing to unpack .../021-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 324s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 324s Selecting previously unselected package libxrender1:armhf. 324s Preparing to unpack .../022-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 324s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 324s Selecting previously unselected package libxft2:armhf. 324s Preparing to unpack .../023-libxft2_2.3.6-1build1_armhf.deb ... 324s Unpacking libxft2:armhf (2.3.6-1build1) ... 324s Selecting previously unselected package libxss1:armhf. 324s Preparing to unpack .../024-libxss1_1%3a1.2.3-1build3_armhf.deb ... 324s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 324s Selecting previously unselected package libtk8.6:armhf. 324s Preparing to unpack .../025-libtk8.6_8.6.16-1_armhf.deb ... 324s Unpacking libtk8.6:armhf (8.6.16-1) ... 324s Selecting previously unselected package tk8.6-blt2.5. 324s Preparing to unpack .../026-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ... 324s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 324s Selecting previously unselected package blt. 324s Preparing to unpack .../027-blt_2.5.3+dfsg-7build1_armhf.deb ... 324s Unpacking blt (2.5.3+dfsg-7build1) ... 324s Selecting previously unselected package libc-dev-bin. 324s Preparing to unpack .../028-libc-dev-bin_2.40-4ubuntu1_armhf.deb ... 324s Unpacking libc-dev-bin (2.40-4ubuntu1) ... 324s Selecting previously unselected package linux-libc-dev:armhf. 324s Preparing to unpack .../029-linux-libc-dev_6.12.0-15.15_armhf.deb ... 324s Unpacking linux-libc-dev:armhf (6.12.0-15.15) ... 324s Selecting previously unselected package libcrypt-dev:armhf. 324s Preparing to unpack .../030-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 324s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 324s Selecting previously unselected package rpcsvc-proto. 324s Preparing to unpack .../031-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 324s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 324s Selecting previously unselected package libc6-dev:armhf. 324s Preparing to unpack .../032-libc6-dev_2.40-4ubuntu1_armhf.deb ... 324s Unpacking libc6-dev:armhf (2.40-4ubuntu1) ... 325s Selecting previously unselected package libisl23:armhf. 325s Preparing to unpack .../033-libisl23_0.27-1_armhf.deb ... 325s Unpacking libisl23:armhf (0.27-1) ... 325s Selecting previously unselected package libmpc3:armhf. 325s Preparing to unpack .../034-libmpc3_1.3.1-1build2_armhf.deb ... 325s Unpacking libmpc3:armhf (1.3.1-1build2) ... 325s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 325s Preparing to unpack .../035-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu1_armhf.deb ... 325s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 325s Selecting previously unselected package cpp-14. 325s Preparing to unpack .../036-cpp-14_14.2.0-17ubuntu1_armhf.deb ... 325s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 325s Selecting previously unselected package cpp-arm-linux-gnueabihf. 325s Preparing to unpack .../037-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 325s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 325s Selecting previously unselected package cpp. 325s Preparing to unpack .../038-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 325s Unpacking cpp (4:14.2.0-1ubuntu1) ... 325s Selecting previously unselected package libcc1-0:armhf. 325s Preparing to unpack .../039-libcc1-0_15-20250213-1ubuntu1_armhf.deb ... 325s Unpacking libcc1-0:armhf (15-20250213-1ubuntu1) ... 325s Selecting previously unselected package libgomp1:armhf. 325s Preparing to unpack .../040-libgomp1_15-20250213-1ubuntu1_armhf.deb ... 325s Unpacking libgomp1:armhf (15-20250213-1ubuntu1) ... 325s Selecting previously unselected package libasan8:armhf. 325s Preparing to unpack .../041-libasan8_15-20250213-1ubuntu1_armhf.deb ... 325s Unpacking libasan8:armhf (15-20250213-1ubuntu1) ... 325s Selecting previously unselected package libubsan1:armhf. 325s Preparing to unpack .../042-libubsan1_15-20250213-1ubuntu1_armhf.deb ... 325s Unpacking libubsan1:armhf (15-20250213-1ubuntu1) ... 325s Selecting previously unselected package libgcc-14-dev:armhf. 325s Preparing to unpack .../043-libgcc-14-dev_14.2.0-17ubuntu1_armhf.deb ... 325s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu1) ... 325s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 325s Preparing to unpack .../044-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu1_armhf.deb ... 325s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 326s Selecting previously unselected package gcc-14. 326s Preparing to unpack .../045-gcc-14_14.2.0-17ubuntu1_armhf.deb ... 326s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 326s Selecting previously unselected package gcc-arm-linux-gnueabihf. 326s Preparing to unpack .../046-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 326s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package gcc. 326s Preparing to unpack .../047-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 326s Unpacking gcc (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package libstdc++-14-dev:armhf. 326s Preparing to unpack .../048-libstdc++-14-dev_14.2.0-17ubuntu1_armhf.deb ... 326s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu1) ... 326s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 326s Preparing to unpack .../049-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu1_armhf.deb ... 326s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 326s Selecting previously unselected package g++-14. 326s Preparing to unpack .../050-g++-14_14.2.0-17ubuntu1_armhf.deb ... 326s Unpacking g++-14 (14.2.0-17ubuntu1) ... 326s Selecting previously unselected package g++-arm-linux-gnueabihf. 326s Preparing to unpack .../051-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 326s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package g++. 326s Preparing to unpack .../052-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 326s Unpacking g++ (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package build-essential. 326s Preparing to unpack .../053-build-essential_12.10ubuntu1_armhf.deb ... 326s Unpacking build-essential (12.10ubuntu1) ... 326s Selecting previously unselected package cython3. 326s Preparing to unpack .../054-cython3_3.0.11+dfsg-2ubuntu1_armhf.deb ... 326s Unpacking cython3 (3.0.11+dfsg-2ubuntu1) ... 326s Selecting previously unselected package libdebhelper-perl. 327s Preparing to unpack .../055-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 327s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 327s Selecting previously unselected package libtool. 327s Preparing to unpack .../056-libtool_2.5.4-3build1_all.deb ... 327s Unpacking libtool (2.5.4-3build1) ... 327s Selecting previously unselected package dh-autoreconf. 327s Preparing to unpack .../057-dh-autoreconf_20_all.deb ... 327s Unpacking dh-autoreconf (20) ... 327s Selecting previously unselected package libarchive-zip-perl. 327s Preparing to unpack .../058-libarchive-zip-perl_1.68-1_all.deb ... 327s Unpacking libarchive-zip-perl (1.68-1) ... 327s Selecting previously unselected package libfile-stripnondeterminism-perl. 327s Preparing to unpack .../059-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 327s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 327s Selecting previously unselected package dh-strip-nondeterminism. 327s Preparing to unpack .../060-dh-strip-nondeterminism_1.14.1-2_all.deb ... 327s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 327s Selecting previously unselected package debugedit. 327s Preparing to unpack .../061-debugedit_1%3a5.1-2_armhf.deb ... 327s Unpacking debugedit (1:5.1-2) ... 327s Selecting previously unselected package dwz. 327s Preparing to unpack .../062-dwz_0.15-1build6_armhf.deb ... 327s Unpacking dwz (0.15-1build6) ... 327s Selecting previously unselected package gettext. 327s Preparing to unpack .../063-gettext_0.23.1-1_armhf.deb ... 327s Unpacking gettext (0.23.1-1) ... 327s Selecting previously unselected package intltool-debian. 327s Preparing to unpack .../064-intltool-debian_0.35.0+20060710.6_all.deb ... 327s Unpacking intltool-debian (0.35.0+20060710.6) ... 327s Selecting previously unselected package po-debconf. 327s Preparing to unpack .../065-po-debconf_1.0.21+nmu1_all.deb ... 327s Unpacking po-debconf (1.0.21+nmu1) ... 327s Selecting previously unselected package debhelper. 327s Preparing to unpack .../066-debhelper_13.24.1ubuntu2_all.deb ... 327s Unpacking debhelper (13.24.1ubuntu2) ... 327s Selecting previously unselected package dh-python. 327s Preparing to unpack .../067-dh-python_6.20250108_all.deb ... 327s Unpacking dh-python (6.20250108) ... 327s Selecting previously unselected package docutils-common. 327s Preparing to unpack .../068-docutils-common_0.21.2+dfsg-2_all.deb ... 327s Unpacking docutils-common (0.21.2+dfsg-2) ... 327s Selecting previously unselected package fonts-font-awesome. 327s Preparing to unpack .../069-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 327s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 327s Selecting previously unselected package fonts-lyx. 327s Preparing to unpack .../070-fonts-lyx_2.4.3-1_all.deb ... 327s Unpacking fonts-lyx (2.4.3-1) ... 327s Selecting previously unselected package fonts-mathjax. 327s Preparing to unpack .../071-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 327s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 327s Selecting previously unselected package libaec0:armhf. 327s Preparing to unpack .../072-libaec0_1.1.3-1_armhf.deb ... 327s Unpacking libaec0:armhf (1.1.3-1) ... 327s Selecting previously unselected package libblas3:armhf. 328s Preparing to unpack .../073-libblas3_3.12.1-2_armhf.deb ... 328s Unpacking libblas3:armhf (3.12.1-2) ... 328s Selecting previously unselected package libpixman-1-0:armhf. 328s Preparing to unpack .../074-libpixman-1-0_0.44.0-3_armhf.deb ... 328s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 328s Selecting previously unselected package libxcb-render0:armhf. 328s Preparing to unpack .../075-libxcb-render0_1.17.0-2_armhf.deb ... 328s Unpacking libxcb-render0:armhf (1.17.0-2) ... 328s Selecting previously unselected package libxcb-shm0:armhf. 328s Preparing to unpack .../076-libxcb-shm0_1.17.0-2_armhf.deb ... 328s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 328s Selecting previously unselected package libcairo2:armhf. 328s Preparing to unpack .../077-libcairo2_1.18.2-2_armhf.deb ... 328s Unpacking libcairo2:armhf (1.18.2-2) ... 328s Selecting previously unselected package libdeflate0:armhf. 328s Preparing to unpack .../078-libdeflate0_1.23-1_armhf.deb ... 328s Unpacking libdeflate0:armhf (1.23-1) ... 328s Selecting previously unselected package libexpat1-dev:armhf. 328s Preparing to unpack .../079-libexpat1-dev_2.6.4-1_armhf.deb ... 328s Unpacking libexpat1-dev:armhf (2.6.4-1) ... 328s Selecting previously unselected package libgfortran5:armhf. 328s Preparing to unpack .../080-libgfortran5_15-20250213-1ubuntu1_armhf.deb ... 328s Unpacking libgfortran5:armhf (15-20250213-1ubuntu1) ... 328s Selecting previously unselected package libgraphite2-3:armhf. 328s Preparing to unpack .../081-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 328s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 328s Selecting previously unselected package libharfbuzz0b:armhf. 328s Preparing to unpack .../082-libharfbuzz0b_10.2.0-1_armhf.deb ... 328s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 328s Selecting previously unselected package libsz2:armhf. 328s Preparing to unpack .../083-libsz2_1.1.3-1_armhf.deb ... 328s Unpacking libsz2:armhf (1.1.3-1) ... 328s Selecting previously unselected package libhdf5-310:armhf. 328s Preparing to unpack .../084-libhdf5-310_1.14.5+repack-3_armhf.deb ... 328s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 328s Selecting previously unselected package libhdf5-hl-310:armhf. 328s Preparing to unpack .../085-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... 328s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... 328s Selecting previously unselected package libimagequant0:armhf. 328s Preparing to unpack .../086-libimagequant0_2.18.0-1build1_armhf.deb ... 328s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 328s Selecting previously unselected package libjpeg-turbo8:armhf. 328s Preparing to unpack .../087-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 328s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 328s Selecting previously unselected package libjpeg8:armhf. 328s Preparing to unpack .../088-libjpeg8_8c-2ubuntu11_armhf.deb ... 328s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 328s Selecting previously unselected package libjs-jquery. 328s Preparing to unpack .../089-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 328s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 328s Selecting previously unselected package libjs-jquery-ui. 328s Preparing to unpack .../090-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 328s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 328s Selecting previously unselected package libjs-underscore. 328s Preparing to unpack .../091-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 328s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 328s Selecting previously unselected package libjs-sphinxdoc. 328s Preparing to unpack .../092-libjs-sphinxdoc_8.1.3-5_all.deb ... 328s Unpacking libjs-sphinxdoc (8.1.3-5) ... 328s Selecting previously unselected package libjson-perl. 328s Preparing to unpack .../093-libjson-perl_4.10000-1_all.deb ... 328s Unpacking libjson-perl (4.10000-1) ... 328s Selecting previously unselected package liblapack3:armhf. 328s Preparing to unpack .../094-liblapack3_3.12.1-2_armhf.deb ... 328s Unpacking liblapack3:armhf (3.12.1-2) ... 328s Selecting previously unselected package liblbfgsb0:armhf. 328s Preparing to unpack .../095-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 328s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 328s Selecting previously unselected package liblcms2-2:armhf. 328s Preparing to unpack .../096-liblcms2-2_2.16-2_armhf.deb ... 328s Unpacking liblcms2-2:armhf (2.16-2) ... 328s Selecting previously unselected package liblerc4:armhf. 328s Preparing to unpack .../097-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 328s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 328s Selecting previously unselected package liblzf1:armhf. 328s Preparing to unpack .../098-liblzf1_3.6-4_armhf.deb ... 328s Unpacking liblzf1:armhf (3.6-4) ... 328s Selecting previously unselected package libnetcdf22:armhf. 329s Preparing to unpack .../099-libnetcdf22_1%3a4.9.3-1_armhf.deb ... 329s Unpacking libnetcdf22:armhf (1:4.9.3-1) ... 329s Selecting previously unselected package libpython3.13:armhf. 329s Preparing to unpack .../100-libpython3.13_3.13.2-1_armhf.deb ... 329s Unpacking libpython3.13:armhf (3.13.2-1) ... 329s Selecting previously unselected package zlib1g-dev:armhf. 329s Preparing to unpack .../101-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 329s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 329s Selecting previously unselected package libpython3.13-dev:armhf. 329s Preparing to unpack .../102-libpython3.13-dev_3.13.2-1_armhf.deb ... 329s Unpacking libpython3.13-dev:armhf (3.13.2-1) ... 329s Selecting previously unselected package libpython3-dev:armhf. 329s Preparing to unpack .../103-libpython3-dev_3.13.1-1~exp2_armhf.deb ... 329s Unpacking libpython3-dev:armhf (3.13.1-1~exp2) ... 329s Selecting previously unselected package libpython3.12t64:armhf. 329s Preparing to unpack .../104-libpython3.12t64_3.12.9-1_armhf.deb ... 329s Unpacking libpython3.12t64:armhf (3.12.9-1) ... 329s Selecting previously unselected package libpython3.12-dev:armhf. 329s Preparing to unpack .../105-libpython3.12-dev_3.12.9-1_armhf.deb ... 329s Unpacking libpython3.12-dev:armhf (3.12.9-1) ... 329s Selecting previously unselected package libpython3-all-dev:armhf. 329s Preparing to unpack .../106-libpython3-all-dev_3.13.1-1~exp2_armhf.deb ... 329s Unpacking libpython3-all-dev:armhf (3.13.1-1~exp2) ... 329s Selecting previously unselected package libqhull-r8.0:armhf. 329s Preparing to unpack .../107-libqhull-r8.0_2020.2-6build1_armhf.deb ... 329s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 329s Selecting previously unselected package libraqm0:armhf. 329s Preparing to unpack .../108-libraqm0_0.10.2-1_armhf.deb ... 329s Unpacking libraqm0:armhf (0.10.2-1) ... 329s Selecting previously unselected package libsharpyuv0:armhf. 329s Preparing to unpack .../109-libsharpyuv0_1.5.0-0.1_armhf.deb ... 329s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 329s Selecting previously unselected package libjbig0:armhf. 329s Preparing to unpack .../110-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 329s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 329s Selecting previously unselected package libwebp7:armhf. 329s Preparing to unpack .../111-libwebp7_1.5.0-0.1_armhf.deb ... 329s Unpacking libwebp7:armhf (1.5.0-0.1) ... 329s Selecting previously unselected package libtiff6:armhf. 329s Preparing to unpack .../112-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 329s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 329s Selecting previously unselected package libwebpdemux2:armhf. 329s Preparing to unpack .../113-libwebpdemux2_1.5.0-0.1_armhf.deb ... 329s Unpacking libwebpdemux2:armhf (1.5.0-0.1) ... 329s Selecting previously unselected package libwebpmux3:armhf. 329s Preparing to unpack .../114-libwebpmux3_1.5.0-0.1_armhf.deb ... 329s Unpacking libwebpmux3:armhf (1.5.0-0.1) ... 329s Selecting previously unselected package libxslt1.1:armhf. 329s Preparing to unpack .../115-libxslt1.1_1.1.39-0exp1ubuntu2_armhf.deb ... 329s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu2) ... 329s Selecting previously unselected package python3-packaging. 329s Preparing to unpack .../116-python3-packaging_24.2-1_all.deb ... 329s Unpacking python3-packaging (24.2-1) ... 330s Selecting previously unselected package python3-pyproject-hooks. 330s Preparing to unpack .../117-python3-pyproject-hooks_1.2.0-1_all.deb ... 330s Unpacking python3-pyproject-hooks (1.2.0-1) ... 330s Selecting previously unselected package python3-toml. 330s Preparing to unpack .../118-python3-toml_0.10.2-1_all.deb ... 330s Unpacking python3-toml (0.10.2-1) ... 330s Selecting previously unselected package python3-wheel. 330s Preparing to unpack .../119-python3-wheel_0.45.1-1_all.deb ... 330s Unpacking python3-wheel (0.45.1-1) ... 330s Selecting previously unselected package python3-build. 330s Preparing to unpack .../120-python3-build_1.2.2-1_all.deb ... 330s Unpacking python3-build (1.2.2-1) ... 330s Selecting previously unselected package python3-installer. 330s Preparing to unpack .../121-python3-installer_0.7.0+dfsg1-3_all.deb ... 330s Unpacking python3-installer (0.7.0+dfsg1-3) ... 330s Selecting previously unselected package pybuild-plugin-pyproject. 330s Preparing to unpack .../122-pybuild-plugin-pyproject_6.20250108_all.deb ... 330s Unpacking pybuild-plugin-pyproject (6.20250108) ... 330s Selecting previously unselected package python-matplotlib-data. 330s Preparing to unpack .../123-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 330s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 330s Selecting previously unselected package libjs-mathjax. 330s Preparing to unpack .../124-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 330s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 330s Selecting previously unselected package python-mdanalysis-doc. 330s Preparing to unpack .../125-python-mdanalysis-doc_2.8.0-2_all.deb ... 330s Unpacking python-mdanalysis-doc (2.8.0-2) ... 331s Selecting previously unselected package python3-all. 331s Preparing to unpack .../126-python3-all_3.13.1-1~exp2_armhf.deb ... 331s Unpacking python3-all (3.13.1-1~exp2) ... 331s Selecting previously unselected package python3.13-dev. 331s Preparing to unpack .../127-python3.13-dev_3.13.2-1_armhf.deb ... 331s Unpacking python3.13-dev (3.13.2-1) ... 331s Selecting previously unselected package python3-dev. 331s Preparing to unpack .../128-python3-dev_3.13.1-1~exp2_armhf.deb ... 331s Unpacking python3-dev (3.13.1-1~exp2) ... 331s Selecting previously unselected package python3.12-dev. 331s Preparing to unpack .../129-python3.12-dev_3.12.9-1_armhf.deb ... 331s Unpacking python3.12-dev (3.12.9-1) ... 331s Selecting previously unselected package python3-all-dev. 331s Preparing to unpack .../130-python3-all-dev_3.13.1-1~exp2_armhf.deb ... 331s Unpacking python3-all-dev (3.13.1-1~exp2) ... 331s Selecting previously unselected package python3-numpy. 331s Preparing to unpack .../131-python3-numpy_1%3a1.26.4+ds-13_armhf.deb ... 331s Unpacking python3-numpy (1:1.26.4+ds-13) ... 331s Selecting previously unselected package python3.12-tk. 331s Preparing to unpack .../132-python3.12-tk_3.12.9-1_armhf.deb ... 331s Unpacking python3.12-tk (3.12.9-1) ... 331s Selecting previously unselected package python3.13-tk. 331s Preparing to unpack .../133-python3.13-tk_3.13.2-1_armhf.deb ... 331s Unpacking python3.13-tk (3.13.2-1) ... 331s Selecting previously unselected package python3-tk:armhf. 331s Preparing to unpack .../134-python3-tk_3.13.1-1_armhf.deb ... 331s Unpacking python3-tk:armhf (3.13.1-1) ... 331s Selecting previously unselected package python3-pil.imagetk:armhf. 331s Preparing to unpack .../135-python3-pil.imagetk_11.1.0-5_armhf.deb ... 331s Unpacking python3-pil.imagetk:armhf (11.1.0-5) ... 331s Selecting previously unselected package libopenjp2-7:armhf. 331s Preparing to unpack .../136-libopenjp2-7_2.5.0-2ubuntu3_armhf.deb ... 331s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu3) ... 331s Selecting previously unselected package python3-pil:armhf. 331s Preparing to unpack .../137-python3-pil_11.1.0-5_armhf.deb ... 331s Unpacking python3-pil:armhf (11.1.0-5) ... 331s Selecting previously unselected package python3-cairo. 331s Preparing to unpack .../138-python3-cairo_1.26.1-2build1_armhf.deb ... 331s Unpacking python3-cairo (1.26.1-2build1) ... 331s Selecting previously unselected package python3-freetype. 331s Preparing to unpack .../139-python3-freetype_2.5.1-1_all.deb ... 331s Unpacking python3-freetype (2.5.1-1) ... 331s Selecting previously unselected package python3-rlpycairo. 331s Preparing to unpack .../140-python3-rlpycairo_0.3.0-3_all.deb ... 331s Unpacking python3-rlpycairo (0.3.0-3) ... 331s Selecting previously unselected package python3-reportlab. 331s Preparing to unpack .../141-python3-reportlab_4.3.0-1_all.deb ... 331s Unpacking python3-reportlab (4.3.0-1) ... 332s Selecting previously unselected package w3c-sgml-lib. 332s Preparing to unpack .../142-w3c-sgml-lib_1.3-3_all.deb ... 332s Unpacking w3c-sgml-lib (1.3-3) ... 332s Selecting previously unselected package python3-biopython. 332s Preparing to unpack .../143-python3-biopython_1.85+dfsg-2_armhf.deb ... 332s Unpacking python3-biopython (1.85+dfsg-2) ... 332s Selecting previously unselected package python3-brotli. 332s Preparing to unpack .../144-python3-brotli_1.1.0-2build3_armhf.deb ... 332s Unpacking python3-brotli (1.1.0-2build3) ... 332s Selecting previously unselected package python3-cftime. 332s Preparing to unpack .../145-python3-cftime_1.6.4-1build2_armhf.deb ... 332s Unpacking python3-cftime (1.6.4-1build2) ... 332s Selecting previously unselected package python3-lxml:armhf. 332s Preparing to unpack .../146-python3-lxml_5.3.1-1_armhf.deb ... 332s Unpacking python3-lxml:armhf (5.3.1-1) ... 332s Selecting previously unselected package python3-citeproc. 332s Preparing to unpack .../147-python3-citeproc_0.6.0-3_all.deb ... 332s Unpacking python3-citeproc (0.6.0-3) ... 332s Selecting previously unselected package python3-contourpy. 332s Preparing to unpack .../148-python3-contourpy_1.3.1-1_armhf.deb ... 332s Unpacking python3-contourpy (1.3.1-1) ... 332s Selecting previously unselected package python3-cycler. 332s Preparing to unpack .../149-python3-cycler_0.12.1-1_all.deb ... 332s Unpacking python3-cycler (0.12.1-1) ... 332s Selecting previously unselected package python3-dateutil. 332s Preparing to unpack .../150-python3-dateutil_2.9.0-3_all.deb ... 332s Unpacking python3-dateutil (2.9.0-3) ... 332s Selecting previously unselected package python3-decorator. 332s Preparing to unpack .../151-python3-decorator_5.1.1-5_all.deb ... 332s Unpacking python3-decorator (5.1.1-5) ... 332s Selecting previously unselected package python3-defusedxml. 332s Preparing to unpack .../152-python3-defusedxml_0.7.1-3_all.deb ... 332s Unpacking python3-defusedxml (0.7.1-3) ... 332s Selecting previously unselected package python3-roman. 332s Preparing to unpack .../153-python3-roman_5.0-1_all.deb ... 332s Unpacking python3-roman (5.0-1) ... 332s Selecting previously unselected package python3-docutils. 332s Preparing to unpack .../154-python3-docutils_0.21.2+dfsg-2_all.deb ... 332s Unpacking python3-docutils (0.21.2+dfsg-2) ... 332s Selecting previously unselected package python3-looseversion. 332s Preparing to unpack .../155-python3-looseversion_1.3.0-3_all.deb ... 332s Unpacking python3-looseversion (1.3.0-3) ... 332s Selecting previously unselected package python3-duecredit. 333s Preparing to unpack .../156-python3-duecredit_0.10.2-2_all.deb ... 333s Unpacking python3-duecredit (0.10.2-2) ... 333s Selecting previously unselected package python3-monotonic. 333s Preparing to unpack .../157-python3-monotonic_1.6-3_all.deb ... 333s Unpacking python3-monotonic (1.6-3) ... 333s Selecting previously unselected package python3-fasteners. 333s Preparing to unpack .../158-python3-fasteners_0.18-2_all.deb ... 333s Unpacking python3-fasteners (0.18-2) ... 333s Selecting previously unselected package python3-pytz. 333s Preparing to unpack .../159-python3-pytz_2025.1-3_all.deb ... 333s Unpacking python3-pytz (2025.1-3) ... 333s Selecting previously unselected package python3-tz. 333s Preparing to unpack .../160-python3-tz_2025.1-3_all.deb ... 333s Unpacking python3-tz (2025.1-3) ... 333s Selecting previously unselected package python3-platformdirs. 333s Preparing to unpack .../161-python3-platformdirs_4.3.6-1_all.deb ... 333s Unpacking python3-platformdirs (4.3.6-1) ... 333s Selecting previously unselected package python3-fs. 333s Preparing to unpack .../162-python3-fs_2.4.16-6_all.deb ... 333s Unpacking python3-fs (2.4.16-6) ... 333s Selecting previously unselected package python3-lz4. 333s Preparing to unpack .../163-python3-lz4_4.4.0+dfsg-1_armhf.deb ... 333s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 333s Selecting previously unselected package python3-scipy. 333s Preparing to unpack .../164-python3-scipy_1.14.1-4ubuntu1_armhf.deb ... 333s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 333s Selecting previously unselected package python3-mpmath. 334s Preparing to unpack .../165-python3-mpmath_1.3.0-1_all.deb ... 334s Unpacking python3-mpmath (1.3.0-1) ... 334s Selecting previously unselected package python3-sympy. 334s Preparing to unpack .../166-python3-sympy_1.13.3-1_all.deb ... 334s Unpacking python3-sympy (1.13.3-1) ... 334s Selecting previously unselected package python3-ufolib2. 334s Preparing to unpack .../167-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 334s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 334s Selecting previously unselected package python3-unicodedata2. 334s Preparing to unpack .../168-python3-unicodedata2_15.1.0+ds-1build2_armhf.deb ... 334s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 334s Selecting previously unselected package unicode-data. 334s Preparing to unpack .../169-unicode-data_15.1.0-1_all.deb ... 334s Unpacking unicode-data (15.1.0-1) ... 334s Selecting previously unselected package python3-fonttools. 334s Preparing to unpack .../170-python3-fonttools_4.55.3-2_armhf.deb ... 334s Unpacking python3-fonttools (4.55.3-2) ... 334s Selecting previously unselected package sphinx-rtd-theme-common. 334s Preparing to unpack .../171-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 334s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 334s Selecting previously unselected package python3-mrcfile. 334s Preparing to unpack .../172-python3-mrcfile_1.5.4-2_all.deb ... 334s Unpacking python3-mrcfile (1.5.4-2) ... 334s Selecting previously unselected package python3-griddataformats. 334s Preparing to unpack .../173-python3-griddataformats_1.0.2-2_all.deb ... 334s Unpacking python3-griddataformats (1.0.2-2) ... 335s Selecting previously unselected package python3-gsd. 335s Preparing to unpack .../174-python3-gsd_3.3.0-1build2_armhf.deb ... 335s Unpacking python3-gsd (3.3.0-1build2) ... 335s Selecting previously unselected package python3-h5py-serial. 335s Preparing to unpack .../175-python3-h5py-serial_3.12.1-1_armhf.deb ... 335s Unpacking python3-h5py-serial (3.12.1-1) ... 335s Selecting previously unselected package python3-h5py. 335s Preparing to unpack .../176-python3-h5py_3.12.1-1_all.deb ... 335s Unpacking python3-h5py (3.12.1-1) ... 335s Selecting previously unselected package python3-sortedcontainers. 335s Preparing to unpack .../177-python3-sortedcontainers_2.4.0-2_all.deb ... 335s Unpacking python3-sortedcontainers (2.4.0-2) ... 335s Selecting previously unselected package python3-hypothesis. 335s Preparing to unpack .../178-python3-hypothesis_6.125.2-1_all.deb ... 335s Unpacking python3-hypothesis (6.125.2-1) ... 335s Selecting previously unselected package python3-imagesize. 335s Preparing to unpack .../179-python3-imagesize_1.4.1-1_all.deb ... 335s Unpacking python3-imagesize (1.4.1-1) ... 335s Selecting previously unselected package python3-iniconfig. 335s Preparing to unpack .../180-python3-iniconfig_1.1.1-2_all.deb ... 335s Unpacking python3-iniconfig (1.1.1-2) ... 335s Selecting previously unselected package python3-joblib. 335s Preparing to unpack .../181-python3-joblib_1.4.2-2_all.deb ... 335s Unpacking python3-joblib (1.4.2-2) ... 335s Selecting previously unselected package python3-kiwisolver. 335s Preparing to unpack .../182-python3-kiwisolver_1.4.7-3_armhf.deb ... 335s Unpacking python3-kiwisolver (1.4.7-3) ... 335s Selecting previously unselected package python3-latexcodec. 335s Preparing to unpack .../183-python3-latexcodec_3.0.0-1_all.deb ... 335s Unpacking python3-latexcodec (3.0.0-1) ... 335s Selecting previously unselected package python3-matplotlib. 335s Preparing to unpack .../184-python3-matplotlib_3.8.3-3ubuntu2_armhf.deb ... 335s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 335s Selecting previously unselected package python3-mda-xdrlib. 335s Preparing to unpack .../185-python3-mda-xdrlib_0.2.0-3_all.deb ... 335s Unpacking python3-mda-xdrlib (0.2.0-3) ... 335s Selecting previously unselected package python3-msgpack. 335s Preparing to unpack .../186-python3-msgpack_1.0.3-3build3_armhf.deb ... 335s Unpacking python3-msgpack (1.0.3-3build3) ... 335s Selecting previously unselected package python3-mmtf. 335s Preparing to unpack .../187-python3-mmtf_1.1.3-1_all.deb ... 335s Unpacking python3-mmtf (1.1.3-1) ... 335s Selecting previously unselected package python3-threadpoolctl. 335s Preparing to unpack .../188-python3-threadpoolctl_3.1.0-1_all.deb ... 335s Unpacking python3-threadpoolctl (3.1.0-1) ... 335s Selecting previously unselected package python3-tqdm. 335s Preparing to unpack .../189-python3-tqdm_4.67.1-2_all.deb ... 335s Unpacking python3-tqdm (4.67.1-2) ... 335s Selecting previously unselected package python3-mdanalysis. 335s Preparing to unpack .../190-python3-mdanalysis_2.8.0-2_armhf.deb ... 335s Unpacking python3-mdanalysis (2.8.0-2) ... 336s Selecting previously unselected package sphinx-common. 336s Preparing to unpack .../191-sphinx-common_8.1.3-5_all.deb ... 336s Unpacking sphinx-common (8.1.3-5) ... 336s Selecting previously unselected package python3-alabaster. 336s Preparing to unpack .../192-python3-alabaster_0.7.16-0.1_all.deb ... 336s Unpacking python3-alabaster (0.7.16-0.1) ... 336s Selecting previously unselected package python3-snowballstemmer. 336s Preparing to unpack .../193-python3-snowballstemmer_2.2.0-4build1_all.deb ... 336s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 336s Selecting previously unselected package python3-sphinx. 336s Preparing to unpack .../194-python3-sphinx_8.1.3-5_all.deb ... 336s Unpacking python3-sphinx (8.1.3-5) ... 336s Selecting previously unselected package python3-sphinxcontrib.jquery. 336s Preparing to unpack .../195-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 336s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 336s Selecting previously unselected package python3-sphinx-rtd-theme. 336s Preparing to unpack .../196-python3-sphinx-rtd-theme_3.0.2+dfsg-2_all.deb ... 336s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 336s Selecting previously unselected package python3-msmb-theme. 336s Preparing to unpack .../197-python3-msmb-theme_1.2.0-4_all.deb ... 336s Unpacking python3-msmb-theme (1.2.0-4) ... 336s Selecting previously unselected package python3-netcdf4. 336s Preparing to unpack .../198-python3-netcdf4_1.7.2-1build3_armhf.deb ... 336s Unpacking python3-netcdf4 (1.7.2-1build3) ... 336s Selecting previously unselected package python3-networkx. 336s Preparing to unpack .../199-python3-networkx_3.2.1-4ubuntu1_all.deb ... 336s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 337s Selecting previously unselected package python3-pandas-lib:armhf. 337s Preparing to unpack .../200-python3-pandas-lib_2.2.3+dfsg-8_armhf.deb ... 337s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-8) ... 337s Selecting previously unselected package python3-pandas. 337s Preparing to unpack .../201-python3-pandas_2.2.3+dfsg-8_all.deb ... 337s Unpacking python3-pandas (2.2.3+dfsg-8) ... 338s Selecting previously unselected package python3-pluggy. 338s Preparing to unpack .../202-python3-pluggy_1.5.0-1_all.deb ... 338s Unpacking python3-pluggy (1.5.0-1) ... 338s Selecting previously unselected package python3-six. 338s Preparing to unpack .../203-python3-six_1.17.0-1_all.deb ... 338s Unpacking python3-six (1.17.0-1) ... 338s Selecting previously unselected package python3-pybtex. 338s Preparing to unpack .../204-python3-pybtex_0.24.0-4_all.deb ... 338s Unpacking python3-pybtex (0.24.0-4) ... 338s Selecting previously unselected package python3-pybtex-docutils. 338s Preparing to unpack .../205-python3-pybtex-docutils_1.0.2-1_all.deb ... 338s Unpacking python3-pybtex-docutils (1.0.2-1) ... 338s Selecting previously unselected package python3-pytest. 338s Preparing to unpack .../206-python3-pytest_8.3.4-1_all.deb ... 338s Unpacking python3-pytest (8.3.4-1) ... 338s Selecting previously unselected package python3-seaborn. 338s Preparing to unpack .../207-python3-seaborn_0.13.2-4.1_all.deb ... 338s Unpacking python3-seaborn (0.13.2-4.1) ... 338s Selecting previously unselected package python3-sklearn-lib:armhf. 338s Preparing to unpack .../208-python3-sklearn-lib_1.4.2+dfsg-7build1_armhf.deb ... 338s Unpacking python3-sklearn-lib:armhf (1.4.2+dfsg-7build1) ... 338s Selecting previously unselected package python3-sklearn. 338s Preparing to unpack .../209-python3-sklearn_1.4.2+dfsg-7build1_all.deb ... 338s Unpacking python3-sklearn (1.4.2+dfsg-7build1) ... 339s Selecting previously unselected package python3-sphinx-sitemap. 339s Preparing to unpack .../210-python3-sphinx-sitemap_2.6.0-1_all.deb ... 339s Unpacking python3-sphinx-sitemap (2.6.0-1) ... 339s Selecting previously unselected package python3-sphinxcontrib.bibtex. 339s Preparing to unpack .../211-python3-sphinxcontrib.bibtex_2.6.2-1_all.deb ... 339s Unpacking python3-sphinxcontrib.bibtex (2.6.2-1) ... 339s Setting up libpython3.13:armhf (3.13.2-1) ... 339s Setting up dh-python (6.20250108) ... 339s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 339s Setting up liblcms2-2:armhf (2.16-2) ... 339s Setting up python3-iniconfig (1.1.1-2) ... 339s Setting up libpixman-1-0:armhf (0.44.0-3) ... 339s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 339s Setting up w3c-sgml-lib (1.3-3) ... 366s Setting up fonts-lato (2.015-1) ... 366s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 366s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 366s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 366s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 366s Setting up python3-joblib (1.4.2-2) ... 367s Setting up python3-lz4 (4.4.0+dfsg-1) ... 367s Setting up libxcb-render0:armhf (1.17.0-2) ... 367s Setting up python3-defusedxml (0.7.1-3) ... 367s Setting up libarchive-zip-perl (1.68-1) ... 367s Setting up python3-alabaster (0.7.16-0.1) ... 367s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 367s Setting up fonts-lyx (2.4.3-1) ... 367s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 367s Setting up python3-tqdm (4.67.1-2) ... 367s Setting up python3-threadpoolctl (3.1.0-1) ... 368s Setting up libpython3.12-minimal:armhf (3.12.9-1) ... 368s Setting up x11-common (1:7.7+23ubuntu3) ... 368s Setting up libdeflate0:armhf (1.23-1) ... 368s Setting up linux-libc-dev:armhf (6.12.0-15.15) ... 368s Setting up m4 (1.4.19-5) ... 368s Setting up python3-latexcodec (3.0.0-1) ... 368s Setting up libqhull-r8.0:armhf (2020.2-6build1) ... 368s Setting up python3-pytz (2025.1-3) ... 368s Setting up libxcb-shm0:armhf (1.17.0-2) ... 368s Setting up python3-sortedcontainers (2.4.0-2) ... 368s Setting up libgomp1:armhf (15-20250213-1ubuntu1) ... 368s Setting up python3-networkx (3.2.1-4ubuntu1) ... 371s Setting up python3-wheel (0.45.1-1) ... 371s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 371s Setting up python3-mda-xdrlib (0.2.0-3) ... 371s Setting up libaec0:armhf (1.1.3-1) ... 371s Setting up python3-platformdirs (4.3.6-1) ... 372s Setting up python3-tz (2025.1-3) ... 372s Setting up python3-monotonic (1.6-3) ... 372s Setting up python3-fs (2.4.16-6) ... 372s Setting up unicode-data (15.1.0-1) ... 372s Setting up python3-six (1.17.0-1) ... 372s Setting up python3-roman (5.0-1) ... 372s Setting up python3-decorator (5.1.1-5) ... 373s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 373s Setting up autotools-dev (20220109.1) ... 373s Setting up libblas3:armhf (3.12.1-2) ... 373s 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 373s Setting up python3-packaging (24.2-1) ... 373s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 373s Setting up python3-pyproject-hooks (1.2.0-1) ... 373s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 373s Setting up python3-snowballstemmer (2.2.0-4build1) ... 373s Setting up python3-brotli (1.1.0-2build3) ... 374s Setting up liblzf1:armhf (3.6-4) ... 374s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 374s Setting up python3-cycler (0.12.1-1) ... 374s Setting up libimagequant0:armhf (2.18.0-1build1) ... 374s Setting up fonts-dejavu-mono (2.37-8) ... 374s Setting up python3-kiwisolver (1.4.7-3) ... 374s Setting up libmpc3:armhf (1.3.1-1build2) ... 374s Setting up cython3 (3.0.11+dfsg-2ubuntu1) ... 376s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 376s Setting up autopoint (0.23.1-1) ... 376s Setting up fonts-dejavu-core (2.37-8) ... 376s Setting up python3-fasteners (0.18-2) ... 376s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 376s Setting up python3-toml (0.10.2-1) ... 376s Setting up python3-installer (0.7.0+dfsg1-3) ... 376s Setting up libgfortran5:armhf (15-20250213-1ubuntu1) ... 376s Setting up autoconf (2.72-3) ... 376s Setting up python3-pluggy (1.5.0-1) ... 376s Setting up libwebp7:armhf (1.5.0-0.1) ... 376s Setting up python3-pybtex (0.24.0-4) ... 377s Setting up libubsan1:armhf (15-20250213-1ubuntu1) ... 377s Setting up dwz (0.15-1build6) ... 377s Setting up python3-looseversion (1.3.0-3) ... 377s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 377s Setting up libasan8:armhf (15-20250213-1ubuntu1) ... 377s Setting up docutils-common (0.21.2+dfsg-2) ... 377s Setting up libjson-perl (4.10000-1) ... 377s Setting up libnsl2:armhf (1.3.0-3build3) ... 377s Setting up libxslt1.1:armhf (1.1.39-0exp1ubuntu2) ... 377s Setting up debugedit (1:5.1-2) ... 377s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu3) ... 377s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 377s Setting up python3-dateutil (2.9.0-3) ... 377s Setting up python3-msgpack (1.0.3-3build3) ... 377s Setting up libxss1:armhf (1:1.2.3-1build3) ... 377s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 377s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu1) ... 377s Setting up python3-mpmath (1.3.0-1) ... 378s Setting up libisl23:armhf (0.27-1) ... 378s Setting up python3-build (1.2.2-1) ... 378s Setting up libc-dev-bin (2.40-4ubuntu1) ... 378s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 378s Setting up libwebpmux3:armhf (1.5.0-0.1) ... 378s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 378s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 378s Setting up libcc1-0:armhf (15-20250213-1ubuntu1) ... 378s Setting up libsz2:armhf (1.1.3-1) ... 378s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 378s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 378s Setting up python3-imagesize (1.4.1-1) ... 379s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 379s Setting up automake (1:1.17-3) ... 379s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 379s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 379s Setting up python3-sympy (1.13.3-1) ... 391s Setting up python3.12-minimal (3.12.9-1) ... 392s Setting up liblapack3:armhf (3.12.1-2) ... 392s 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 392s Setting up gettext (0.23.1-1) ... 392s Setting up libpython3.12-stdlib:armhf (3.12.9-1) ... 392s Setting up pybuild-plugin-pyproject (6.20250108) ... 392s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 393s Setting up python3-pytest (8.3.4-1) ... 393s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 393s Setting up python3.12 (3.12.9-1) ... 395s Setting up python3-hypothesis (6.125.2-1) ... 396s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 396s Setting up python3-all (3.13.1-1~exp2) ... 396s Setting up python3-freetype (2.5.1-1) ... 396s Setting up xfonts-utils (1:7.7+7) ... 396s Setting up intltool-debian (0.35.0+20060710.6) ... 396s Setting up libpython3.12t64:armhf (3.12.9-1) ... 396s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 396s Setting up libraqm0:armhf (0.10.2-1) ... 396s Setting up python3-numpy (1:1.26.4+ds-13) ... 400s Setting up libjs-sphinxdoc (8.1.3-5) ... 400s Setting up cpp-14 (14.2.0-17ubuntu1) ... 400s Setting up dh-strip-nondeterminism (1.14.1-2) ... 400s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 400s Setting up python3-lxml:armhf (5.3.1-1) ... 400s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 400s Setting up libc6-dev:armhf (2.40-4ubuntu1) ... 400s Setting up python3-contourpy (1.3.1-1) ... 400s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu1) ... 400s Setting up cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 400s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 400s Setting up gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 400s Setting up python3-mrcfile (1.5.4-2) ... 400s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... 400s Setting up g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu1) ... 400s Setting up python3-scipy (1.14.1-4ubuntu1) ... 408s Setting up python3-citeproc (0.6.0-3) ... 408s Setting up po-debconf (1.0.21+nmu1) ... 408s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-8) ... 408s Setting up libnetcdf22:armhf (1:4.9.3-1) ... 408s Setting up python3-sklearn-lib:armhf (1.4.2+dfsg-7build1) ... 408s Setting up python3-h5py-serial (3.12.1-1) ... 408s Setting up python3-gsd (3.3.0-1build2) ... 408s Setting up python3-mmtf (1.1.3-1) ... 409s Setting up fonts-urw-base35 (20200910-8) ... 409s Setting up python-mdanalysis-doc (2.8.0-2) ... 409s Setting up gcc-14 (14.2.0-17ubuntu1) ... 409s Setting up python3-pil:armhf (11.1.0-5) ... 410s Setting up python3-griddataformats (1.0.2-2) ... 410s Setting up libexpat1-dev:armhf (2.6.4-1) ... 410s Setting up python3-pandas (2.2.3+dfsg-8) ... 420s Setting up sphinx-common (8.1.3-5) ... 420s Setting up python3-h5py (3.12.1-1) ... 420s Setting up python3-sklearn (1.4.2+dfsg-7build1) ... 424s Setting up python3-cftime (1.6.4-1build2) ... 424s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 424s Setting up cpp (4:14.2.0-1ubuntu1) ... 424s Setting up g++-14 (14.2.0-17ubuntu1) ... 424s Setting up python3-netcdf4 (1.7.2-1build3) ... 425s Setting up g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 425s Setting up python3-duecredit (0.10.2-2) ... 425s Setting up libtool (2.5.4-3build1) ... 425s Setting up libpython3.12-dev:armhf (3.12.9-1) ... 425s Setting up gcc (4:14.2.0-1ubuntu1) ... 425s Setting up dh-autoreconf (20) ... 425s Setting up libpython3.13-dev:armhf (3.13.2-1) ... 425s Setting up python3.12-dev (3.12.9-1) ... 425s Setting up g++ (4:14.2.0-1ubuntu1) ... 425s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 425s Setting up build-essential (12.10ubuntu1) ... 425s Setting up libpython3-dev:armhf (3.13.1-1~exp2) ... 425s Setting up python3.13-dev (3.13.2-1) ... 425s Setting up debhelper (13.24.1ubuntu2) ... 425s Setting up libpython3-all-dev:armhf (3.13.1-1~exp2) ... 425s Setting up python3-dev (3.13.1-1~exp2) ... 425s Setting up python3-all-dev (3.13.1-1~exp2) ... 425s Setting up python3-fonttools (4.55.3-2) ... 427s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 427s Processing triggers for sgml-base (1.31) ... 427s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 427s Setting up python3-docutils (0.21.2+dfsg-2) ... 428s Processing triggers for install-info (7.1.1-1) ... 428s Setting up libxft2:armhf (2.3.6-1build1) ... 428s Setting up libtk8.6:armhf (8.6.16-1) ... 428s Processing triggers for libc-bin (2.40-4ubuntu1) ... 428s Setting up python3.12-tk (3.12.9-1) ... 428s Processing triggers for systemd (257.2-3ubuntu1) ... 428s Processing triggers for man-db (2.13.0-1) ... 429s Setting up libcairo2:armhf (1.18.2-2) ... 429s Setting up python3.13-tk (3.13.2-1) ... 429s Setting up python3-pybtex-docutils (1.0.2-1) ... 429s Setting up python3-sphinx (8.1.3-5) ... 431s Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... 431s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 431s Setting up python3-cairo (1.26.1-2build1) ... 431s Setting up python3-sphinx-sitemap (2.6.0-1) ... 431s Setting up blt (2.5.3+dfsg-7build1) ... 431s Setting up python3-tk:armhf (3.13.1-1) ... 431s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 432s Setting up python3-pil.imagetk:armhf (11.1.0-5) ... 432s Setting up python3-rlpycairo (0.3.0-3) ... 432s Setting up python3-reportlab (4.3.0-1) ... 433s Setting up python3-biopython (1.85+dfsg-2) ... 436s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 439s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 439s Setting up python3-mdanalysis (2.8.0-2) ... 440s Setting up python3-seaborn (0.13.2-4.1) ... 440s Setting up python3-msmb-theme (1.2.0-4) ... 440s Processing triggers for libc-bin (2.40-4ubuntu1) ... 453s autopkgtest [12:10:04]: test test-mdanalysis: [----------------------- 455s skipping tests with SKIP_TEST_LIST=test_all_import[.analysis.hole2] journal.pcbi.1004568 465s ============================= test session starts ============================== 465s platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0 465s rootdir: /tmp/autopkgtest.MV1swv/build.5yX/src 465s plugins: typeguard-4.4.1, hypothesis-6.125.2 465s collected 19663 items / 2 deselected / 6 skipped / 19661 selected 465s 470s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [ 0%] 485s .....................s.ss.s........ [ 0%] 485s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ... [ 0%] 485s testsuite/MDAnalysisTests/analysis/test_backends.py .......... [ 0%] 493s testsuite/MDAnalysisTests/analysis/test_base.py ........................ [ 0%] 513s ....................................................................... [ 0%] 516s testsuite/MDAnalysisTests/analysis/test_bat.py ................... [ 0%] 518s testsuite/MDAnalysisTests/analysis/test_contacts.py .................... [ 1%] 538s ................ [ 1%] 538s testsuite/MDAnalysisTests/analysis/test_data.py . [ 1%] 538s testsuite/MDAnalysisTests/analysis/test_density.py ..................... [ 1%] 545s ...................... [ 1%] 546s testsuite/MDAnalysisTests/analysis/test_dielectric.py ...... [ 1%] 551s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py ........... [ 1%] 559s testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [ 1%] 566s ....................... [ 1%] 572s testsuite/MDAnalysisTests/analysis/test_distances.py ............ [ 1%] 577s testsuite/MDAnalysisTests/analysis/test_dssp.py ........................ [ 1%] 588s ........................................................................ [ 2%] 592s ................ [ 2%] 624s testsuite/MDAnalysisTests/analysis/test_encore.py ..................X..X [ 2%] 644s ...................................... [ 2%] 666s testsuite/MDAnalysisTests/analysis/test_gnm.py .......... [ 2%] 667s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py .............. [ 2%] 668s ................................ [ 2%] 668s testsuite/MDAnalysisTests/analysis/test_hole2.py s [ 2%] 669s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [ 2%] 669s ......... [ 2%] 669s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [ 2%] 670s ................. [ 3%] 670s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py ...... [ 3%] 672s .................................................................... [ 3%] 673s testsuite/MDAnalysisTests/analysis/test_leaflet.py s............ [ 3%] 673s testsuite/MDAnalysisTests/analysis/test_lineardensity.py ........ [ 3%] 676s testsuite/MDAnalysisTests/analysis/test_msd.py .......................ss [ 3%] 676s sssssssssssssssssssssssssssss [ 3%] 677s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [ 3%] 677s [ 3%] 678s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py .................... [ 3%] 678s .............. [ 4%] 681s testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [ 4%] 681s ......................... [ 4%] 684s testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [ 4%] 685s ....... [ 4%] 685s testsuite/MDAnalysisTests/analysis/test_psa.py s [ 4%] 685s testsuite/MDAnalysisTests/analysis/test_rdf.py .................... [ 4%] 686s testsuite/MDAnalysisTests/analysis/test_rdf_s.py ..................... [ 4%] 686s testsuite/MDAnalysisTests/analysis/test_results.py ..................... [ 4%] 686s ........................................................................ [ 5%] 686s ........................................... [ 5%] 703s testsuite/MDAnalysisTests/analysis/test_rms.py ......................... [ 5%] 712s ................................... [ 5%] 712s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py s [ 5%] 713s testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [ 5%] 713s ........................... [ 5%] 713s testsuite/MDAnalysisTests/auxiliary/test_core.py ..... [ 5%] 713s testsuite/MDAnalysisTests/auxiliary/test_edr.py .sssssssssssssssssssssss [ 6%] 713s ssssssssssssssssssssssssssssssssssssssssssss [ 6%] 713s testsuite/MDAnalysisTests/auxiliary/test_xvg.py ........................ [ 6%] 713s ........................................................................ [ 6%] 713s .... [ 6%] 713s testsuite/MDAnalysisTests/converters/test_base.py .. [ 6%] 713s testsuite/MDAnalysisTests/converters/test_rdkit.py .ssssssssssssssssssss [ 6%] 713s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 7%] 713s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 7%] 713s ssssssssssssssssssssssssssssss [ 7%] 713s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ... [ 7%] 717s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [ 7%] 728s ........................................................ [ 8%] 729s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [ 8%] 736s ...............................................................ss.ss.s.s [ 8%] 746s s.sss....ss...s.ssss.ss.s.ss.sss....ss...s.ssss.ss.s.ss.sss....ss.s.ssss [ 8%] 751s .......................................................s [ 9%] 752s testsuite/MDAnalysisTests/coordinates/test_crd.py .............. [ 9%] 752s testsuite/MDAnalysisTests/coordinates/test_dcd.py ...................... [ 9%] 755s .......x.......ss....................................................... [ 9%] 757s ..........................................s [ 9%] 757s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [ 10%] 757s .................................... [ 10%] 758s testsuite/MDAnalysisTests/coordinates/test_dms.py ......... [ 10%] 758s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [ 10%] 758s ....... [ 10%] 758s testsuite/MDAnalysisTests/coordinates/test_gms.py .................. [ 10%] 760s testsuite/MDAnalysisTests/coordinates/test_gro.py ...................... [ 10%] 761s .......................sss.............................................. [ 11%] 762s ..............sss...................................................sss. [ 11%] 781s ..................................................sss................... [ 11%] 792s .................... [ 11%] 792s testsuite/MDAnalysisTests/coordinates/test_gsd.py ss.... [ 11%] 793s testsuite/MDAnalysisTests/coordinates/test_h5md.py ..................... [ 11%] 798s ..............ss........................................................ [ 12%] 815s .......x..................................................... [ 12%] 816s testsuite/MDAnalysisTests/coordinates/test_lammps.py ................... [ 12%] 824s ........................................................................ [ 13%] 856s ................................................................. [ 13%] 859s testsuite/MDAnalysisTests/coordinates/test_memory.py ................... [ 13%] 870s ........x......xxx...................................................... [ 13%] 870s .......................... [ 14%] 870s testsuite/MDAnalysisTests/coordinates/test_mmtf.py ............ [ 14%] 871s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 14%] 871s [ 14%] 872s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 14%] 872s ..... [ 14%] 872s testsuite/MDAnalysisTests/coordinates/test_netcdf.py ................... [ 14%] 875s ........................................................................ [ 14%] 879s ........................................................................ [ 15%] 879s .................. [ 15%] 879s testsuite/MDAnalysisTests/coordinates/test_null.py . [ 15%] 881s testsuite/MDAnalysisTests/coordinates/test_pdb.py ...................... [ 15%] 905s ........................................................................ [ 15%] 909s ........................................................................ [ 16%] 909s ................ [ 16%] 910s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py ............... [ 16%] 911s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 16%] 912s ........ [ 16%] 912s testsuite/MDAnalysisTests/coordinates/test_reader_api.py ............... [ 16%] 912s ........................................................................ [ 16%] 912s ........................................................................ [ 17%] 912s ............................. [ 17%] 912s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py ............. [ 17%] 912s ........................................................................ [ 17%] 915s ........................................................................ [ 18%] 917s ................. [ 18%] 917s testsuite/MDAnalysisTests/coordinates/test_tng.py ..ssssssssssssssssssss [ 18%] 917s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 18%] 917s s [ 18%] 917s testsuite/MDAnalysisTests/coordinates/test_trc.py ...................... [ 18%] 917s .......... [ 18%] 917s testsuite/MDAnalysisTests/coordinates/test_trj.py ...................... [ 19%] 918s .............. [ 19%] 919s testsuite/MDAnalysisTests/coordinates/test_trz.py ...................... [ 19%] 920s .. [ 19%] 920s testsuite/MDAnalysisTests/coordinates/test_txyz.py ...... [ 19%] 920s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 19%] 921s ........................................................... [ 19%] 921s testsuite/MDAnalysisTests/coordinates/test_writer_api.py .ss............ [ 19%] 921s ......ss.....s............ss.....s........... [ 19%] 921s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py .... [ 19%] 923s testsuite/MDAnalysisTests/coordinates/test_xdr.py ...................... [ 20%] 935s ........................................................................ [ 20%] 936s ....ss.................................................................. [ 20%] 937s .ss......................................................... [ 21%] 937s testsuite/MDAnalysisTests/coordinates/test_xyz.py ...................... [ 21%] 937s ...............ss....................................................... [ 21%] 938s .................ss....................................... [ 21%] 938s testsuite/MDAnalysisTests/core/test_accessors.py ssss..s [ 21%] 939s testsuite/MDAnalysisTests/core/test_accumulate.py ...................... [ 22%] 947s ................................................................... [ 22%] 949s testsuite/MDAnalysisTests/core/test_atom.py .................... [ 22%] 954s testsuite/MDAnalysisTests/core/test_atomgroup.py ....................... [ 22%] 966s ........................................................................ [ 22%] 968s ........................................................................ [ 23%] 980s ........................................................................ [ 23%] 1000s ........................................................................ [ 24%] 1017s ........................................................................ [ 24%] 1022s .......................................................... [ 24%] 1023s testsuite/MDAnalysisTests/core/test_atomselections.py .................. [ 24%] 1023s ........................................................................ [ 25%] 1024s ........................................................................ [ 25%] 1040s ..................sssssssssssssssssss................................... [ 25%] 1041s ........................................................................ [ 26%] 1041s ........................................................................ [ 26%] 1042s ........................................................................ [ 26%] 1053s .....................................sssss...........ssssss.... [ 27%] 1053s testsuite/MDAnalysisTests/core/test_copying.py ......................... [ 27%] 1054s .................... [ 27%] 1055s testsuite/MDAnalysisTests/core/test_fragments.py ................ [ 27%] 1055s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%] 1058s ................................................. [ 27%] 1058s testsuite/MDAnalysisTests/core/test_groups.py .......................... [ 28%] 1058s ........................................................................ [ 28%] 1059s ........................................................................ [ 28%] 1059s ........................................................................ [ 29%] 1061s ........................................................................ [ 29%] 1061s ........................................................................ [ 29%] 1061s ........................................................................ [ 30%] 1061s ........................................................................ [ 30%] 1082s ....................................................................... [ 31%] 1082s testsuite/MDAnalysisTests/core/test_index_dtype.py ............... [ 31%] 1082s testsuite/MDAnalysisTests/core/test_requires.py .... [ 31%] 1082s testsuite/MDAnalysisTests/core/test_residue.py .... [ 31%] 1084s testsuite/MDAnalysisTests/core/test_residuegroup.py s..................s [ 31%] 1085s ssss..... [ 31%] 1085s testsuite/MDAnalysisTests/core/test_segment.py ....... [ 31%] 1087s testsuite/MDAnalysisTests/core/test_segmentgroup.py ........... [ 31%] 1087s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%] 1087s ........................................ [ 31%] 1088s testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%] 1088s ...................................................................x.... [ 32%] 1089s ........................................................ [ 32%] 1089s testsuite/MDAnalysisTests/core/test_topologyobjects.py ................. [ 32%] 1093s ...................................................................... [ 32%] 1094s testsuite/MDAnalysisTests/core/test_universe.py .................sssssss [ 33%] 1100s s....................................................................... [ 33%] 1102s ........................................................................ [ 33%] 1106s ........................................................................ [ 34%] 1108s .................................... [ 34%] 1108s testsuite/MDAnalysisTests/core/test_unwrap.py .......................... [ 34%] 1109s ........................................................................ [ 34%] 1109s ........................................................................ [ 35%] 1110s ........................................................................ [ 35%] 1110s ........................................................................ [ 35%] 1111s ........................................................................ [ 36%] 1111s ........................................................................ [ 36%] 1111s ................................................... [ 36%] 1114s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py .............. [ 36%] 1114s . [ 36%] 1115s testsuite/MDAnalysisTests/core/test_wrap.py ............................ [ 37%] 1115s ........................................................................ [ 37%] 1116s ........................................................................ [ 37%] 1116s ........................................................................ [ 38%] 1117s ........................................................................ [ 38%] 1117s ........................................................................ [ 38%] 1117s ........................................................................ [ 39%] 1118s ......................................................... [ 39%] 1118s testsuite/MDAnalysisTests/formats/test_libdcd.py ....................... [ 39%] 1120s ........................................................................ [ 40%] 1120s ...... [ 40%] 1120s testsuite/MDAnalysisTests/formats/test_libmdaxdr.py .................... [ 40%] 1121s ........................................................................ [ 40%] 1121s ... [ 40%] 1158s testsuite/MDAnalysisTests/guesser/test_base.py ........................ [ 40%] 1158s testsuite/MDAnalysisTests/guesser/test_default_guesser.py .............. [ 40%] 1159s ...........................sssssssssss [ 40%] 1163s testsuite/MDAnalysisTests/import/test_import.py .. [ 40%] 1163s testsuite/MDAnalysisTests/lib/test_augment.py .......................... [ 41%] 1163s .......... [ 41%] 1163s testsuite/MDAnalysisTests/lib/test_cutil.py ............. [ 41%] 1163s testsuite/MDAnalysisTests/lib/test_distances.py ........................ [ 41%] 1163s ........................................................................ [ 41%] 1163s ........................................................................ [ 42%] 1163s ........................................................................ [ 42%] 1164s ........................................................................ [ 42%] 1164s ........................................................................ [ 43%] 1164s ........................................................................ [ 43%] 1172s ........................................................................ [ 43%] 1175s ........................................................................ [ 44%] 1175s ........................................................................ [ 44%] 1175s ........................................................................ [ 45%] 1176s ........................................................................ [ 45%] 1176s ........................................................................ [ 45%] 1176s ........................................................................ [ 46%] 1176s ........................................................................ [ 46%] 1177s ........................................................................ [ 46%] 1177s ........................................................................ [ 47%] 1177s ........................................................................ [ 47%] 1177s ........................................................................ [ 47%] 1177s ........................................................................ [ 48%] 1177s ........................................................................ [ 48%] 1177s ........................................................................ [ 49%] 1177s ........................................................................ [ 49%] 1178s ........................................................................ [ 49%] 1178s ........................................................................ [ 50%] 1178s ........................................................................ [ 50%] 1178s ........................................................................ [ 50%] 1178s ........................................................................ [ 51%] 1178s ........................................................................ [ 51%] 1178s ........................................................................ [ 51%] 1178s ........................................................................ [ 52%] 1179s ........................................................................ [ 52%] 1179s ........................................................................ [ 53%] 1179s ........................................................................ [ 53%] 1179s ........................................................................ [ 53%] 1179s ............................................... [ 54%] 1179s testsuite/MDAnalysisTests/lib/test_log.py ... [ 54%] 1179s testsuite/MDAnalysisTests/lib/test_neighborsearch.py .. [ 54%] 1185s testsuite/MDAnalysisTests/lib/test_nsgrid.py ........................... [ 54%] 1185s ..s [ 54%] 1185s testsuite/MDAnalysisTests/lib/test_pkdtree.py ................. [ 54%] 1186s testsuite/MDAnalysisTests/lib/test_qcprot.py .... [ 54%] 1186s testsuite/MDAnalysisTests/lib/test_util.py ............................. [ 54%] 1186s ........................................................................ [ 54%] 1186s ........................................................................ [ 55%] 1186s ........................................................................ [ 55%] 1186s ........................................................................ [ 55%] 1186s ........................................................................ [ 56%] 1186s ........................................................................ [ 56%] 1186s ........................................................................ [ 57%] 1186s ........................................................................ [ 57%] 1186s ........................................................................ [ 57%] 1187s ........................................................................ [ 58%] 1187s ........................................................................ [ 58%] 1187s ........................................................................ [ 58%] 1187s ........................................................................ [ 59%] 1187s ........................................................................ [ 59%] 1187s ........................................................................ [ 59%] 1187s ........................................................................ [ 60%] 1187s ........................................................................ [ 60%] 1187s ........................................................................ [ 61%] 1187s ........................................................................ [ 61%] 1187s ........................................................................ [ 61%] 1188s ........................................................................ [ 62%] 1188s ........................................................................ [ 62%] 1188s ........................................................................ [ 62%] 1188s ........................................................................ [ 63%] 1188s ........................................................................ [ 63%] 1188s ........................................................................ [ 63%] 1188s ........................................................................ [ 64%] 1188s ........................................................................ [ 64%] 1188s ........................................................................ [ 65%] 1189s ........................................................................ [ 65%] 1189s ........................................................................ [ 65%] 1189s ........................................................................ [ 66%] 1189s ........................................................................ [ 66%] 1189s ........................................................................ [ 66%] 1189s ........................................................................ [ 67%] 1189s ........................................................................ [ 67%] 1189s ........................................................................ [ 68%] 1189s ........................................................................ [ 68%] 1190s ........................................................................ [ 68%] 1190s ........................................................................ [ 69%] 1190s ........................................................................ [ 69%] 1190s ........................................................................ [ 69%] 1190s ........................................................................ [ 70%] 1190s ........................................................................ [ 70%] 1190s ........................................................................ [ 70%] 1190s ........................................................................ [ 71%] 1190s ........................................................................ [ 71%] 1190s ........................................................................ [ 72%] 1191s ........................................................................ [ 72%] 1191s ........................................................................ [ 72%] 1191s ........................................................................ [ 73%] 1191s ........................................................................ [ 73%] 1191s ........................................................................ [ 73%] 1191s ........................................................................ [ 74%] 1191s ........................................................................ [ 74%] 1191s ........................................................................ [ 74%] 1191s ........................................................................ [ 75%] 1191s ........................................................................ [ 75%] 1192s ........................................................................ [ 76%] 1192s ........................................................................ [ 76%] 1192s ........................................................................ [ 76%] 1192s ........................................................................ [ 77%] 1192s ........................................................................ [ 77%] 1192s ........................................................................ [ 77%] 1192s ........................................................................ [ 78%] 1192s ........................................................................ [ 78%] 1192s ........................................................................ [ 79%] 1192s ........................................................................ [ 79%] 1192s ........................................................................ [ 79%] 1193s ........................................................................ [ 80%] 1193s ........................................................................ [ 80%] 1194s ........................................................................ [ 80%] 1194s ........................................................................ [ 81%] 1194s ........................................................................ [ 81%] 1194s ........................................................................ [ 81%] 1194s ........................................................................ [ 82%] 1194s ........................................................................ [ 82%] 1194s ........................................................................ [ 83%] 1194s ........................................................................ [ 83%] 1194s .........................................s.............................. [ 83%] 1195s ........................................................................ [ 84%] 1195s .............s.......................................................... [ 84%] 1202s ........................................................................ [ 84%] 1202s ..................................................... [ 85%] 1205s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py .......... [ 85%] 1225s ....................................... [ 85%] 1225s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py .... [ 85%] 1226s .... [ 85%] 1226s testsuite/MDAnalysisTests/test_api.py ................................. [ 85%] 1231s testsuite/MDAnalysisTests/topology/test_altloc.py ... [ 85%] 1232s testsuite/MDAnalysisTests/topology/test_crd.py .......... [ 85%] 1232s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 85%] 1232s .............................................. [ 86%] 1233s testsuite/MDAnalysisTests/topology/test_dms.py ...................... [ 86%] 1233s testsuite/MDAnalysisTests/topology/test_fhiaims.py ............ [ 86%] 1233s testsuite/MDAnalysisTests/topology/test_gms.py ......................... [ 86%] 1233s ......... [ 86%] 1236s testsuite/MDAnalysisTests/topology/test_gro.py ................. [ 86%] 1236s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%] 1236s ...... [ 86%] 1236s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 86%] 1237s ..............ssssssssss..........s [ 86%] 1237s testsuite/MDAnalysisTests/topology/test_hoomdxml.py .................. [ 86%] 1237s testsuite/MDAnalysisTests/topology/test_itp.py ......................... [ 87%] 1237s ........................................................................ [ 87%] 1238s ......................................... [ 87%] 1242s testsuite/MDAnalysisTests/topology/test_lammpsdata.py .................. [ 87%] 1243s ........................................................................ [ 88%] 1243s ........................................................... [ 88%] 1244s testsuite/MDAnalysisTests/topology/test_minimal.py ..................... [ 88%] 1244s ........... [ 88%] 1244s testsuite/MDAnalysisTests/topology/test_mmtf.py ........................ [ 88%] 1244s .............................................. [ 88%] 1244s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%] 1244s ........ [ 89%] 1248s testsuite/MDAnalysisTests/topology/test_pdb.py ......................... [ 89%] 1249s ........................... [ 89%] 1249s testsuite/MDAnalysisTests/topology/test_pdbqt.py .......... [ 89%] 1250s testsuite/MDAnalysisTests/topology/test_pqr.py ........................ [ 89%] 1256s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%] 1259s ........................................ [ 89%] 1259s testsuite/MDAnalysisTests/topology/test_tables.py . [ 89%] 1260s testsuite/MDAnalysisTests/topology/test_top.py ......................... [ 90%] 1265s ........................................................................ [ 90%] 1266s ........................................................................ [ 90%] 1266s ........... [ 90%] 1266s testsuite/MDAnalysisTests/topology/test_topology_base.py ... [ 90%] 1266s testsuite/MDAnalysisTests/topology/test_topology_str_types.py .......... [ 90%] 1273s ........................................................................ [ 91%] 1275s .................. [ 91%] 1280s testsuite/MDAnalysisTests/topology/test_tprparser.py ................... [ 91%] 1288s ........................................................................ [ 91%] 1297s ........................................................................ [ 92%] 1306s ........................................................................ [ 92%] 1314s ........................................................................ [ 92%] 1323s ........................................................................ [ 93%] 1323s ........................................................................ [ 93%] 1324s ........................................................................ [ 93%] 1324s ........................................................................ [ 94%] 1324s ........................................................................ [ 94%] 1324s ........................................................................ [ 95%] 1324s ........................................................................ [ 95%] 1326s ........................................................................ [ 95%] 1328s .................................... [ 95%] 1328s testsuite/MDAnalysisTests/topology/test_txyz.py ....................... [ 96%] 1328s testsuite/MDAnalysisTests/topology/test_xpdb.py .......... [ 96%] 1329s testsuite/MDAnalysisTests/topology/test_xyz.py ......................... [ 96%] 1329s ... [ 96%] 1329s testsuite/MDAnalysisTests/transformations/test_base.py ..... [ 96%] 1329s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%] 1329s ...... [ 96%] 1329s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%] 1329s ......................................... [ 96%] 1331s testsuite/MDAnalysisTests/transformations/test_nojump.py ............ [ 96%] 1331s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%] 1331s . [ 96%] 1331s testsuite/MDAnalysisTests/transformations/test_rotate.py ............... [ 96%] 1331s ............................ [ 97%] 1331s testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%] 1331s ............ [ 97%] 1340s testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%] 1340s ....... [ 97%] 1340s testsuite/MDAnalysisTests/utils/test_authors.py . [ 97%] 1340s testsuite/MDAnalysisTests/utils/test_datafiles.py .... [ 97%] 1340s testsuite/MDAnalysisTests/utils/test_duecredit.py ........... [ 97%] 1340s testsuite/MDAnalysisTests/utils/test_failure.py . [ 97%] 1340s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%] 1340s ........................................................................ [ 97%] 1340s ........................................................................ [ 98%] 1340s ............................................. [ 98%] 1340s testsuite/MDAnalysisTests/utils/test_log.py . [ 98%] 1340s testsuite/MDAnalysisTests/utils/test_meta.py .... [ 98%] 1341s testsuite/MDAnalysisTests/utils/test_modelling.py ............. [ 98%] 1342s testsuite/MDAnalysisTests/utils/test_persistence.py ....... [ 98%] 1354s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%] 1354s ..............ss.. [ 98%] 1354s testsuite/MDAnalysisTests/utils/test_qcprot.py ...... [ 98%] 1357s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%] 1357s [ 98%] 1357s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 99%] 1357s ............... [ 99%] 1357s testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%] 1357s ........................................................................ [ 99%] 1357s ........................................................ [ 99%] 1357s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%] 1357s ....... [ 99%] 1358s testsuite/MDAnalysisTests/visualization/test_streamlines.py ... [100%] 1358s 1358s = 19100 passed, 558 skipped, 2 deselected, 7 xfailed, 2 xpassed, 104647 warnings in 902.86s (0:15:02) = 1380s 1380s DueCredit Report: 1380s - Molecular simulation analysis library / MDAnalysis (v 2.8.0) [1, 2] 1380s - Iterative Calculation of Opimal Reference / MDAnalysis.analysis.align.iterative_average (v 2.8.0) [3] 1380s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.8.0) [4] 1380s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.8.0) [5] 1380s - DSSP algorithm description / MDAnalysis.analysis.dssp (v 2.8.0) [6] 1380s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.8.0) [7] 1380s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.8.0) [8] 1380s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.8.0) [9] 1380s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.8.0) [2] 1380s - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.8.0) [10, 11] 1380s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.8.0) [12] 1380s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 2.8.0, 1.1) [13, 14] 1380s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.8.0) [15] 1380s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.8.0) [16] 1380s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.8.0) [17, 18] 1380s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.8.0) [15] 1380s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.8.0) [19] 1380s - Scientific tools library / numpy (v 1.26.4) [20] 1380s 1380s 2 packages cited 1380s 16 modules cited 1380s 0 functions cited 1380s 1380s References 1380s ---------- 1380s 1380s [1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy. SciPy, pp. 98–105. 1380s [2] Michaud‐Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327. 1380s [3] Linke, M., Köfinger, J. & Hummer, G., 2018. Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 122(21), pp.5630–5639. 1380s [4] Minh, D.D.L., 2019. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. Journal of Computational Chemistry, 41(7), pp.715–730. 1380s [5] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1380s [6] Kabsch, W. & Sander, C., 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers, 22(12), pp.2577–2637. 1380s [7] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1380s [8] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857. 1380s [9] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22). 1380s [10] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877. 1380s [11] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232. 1380s [12] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330. 1380s [13] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy. SciPy, pp. 40–48. 1380s [14] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553. 1380s [15] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575. 1380s [16] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269. 1380s [17] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480. 1380s [18] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563. 1380s [19] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171. 1380s [20] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. 1393s ============================= test session starts ============================== 1393s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 1393s rootdir: /tmp/autopkgtest.MV1swv/build.5yX/src 1393s plugins: typeguard-4.4.1, hypothesis-6.125.2 1393s collected 19667 items / 2 deselected / 6 skipped / 19665 selected 1393s 1397s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [ 0%] 1412s .....................s.ss.s........ [ 0%] 1412s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ... [ 0%] 1412s testsuite/MDAnalysisTests/analysis/test_backends.py .......... [ 0%] 1420s testsuite/MDAnalysisTests/analysis/test_base.py ........................ [ 0%] 1432s ...........................................................FFFFF....... [ 0%] 1434s testsuite/MDAnalysisTests/analysis/test_bat.py .EEFEEEE........... [ 0%] 1436s testsuite/MDAnalysisTests/analysis/test_contacts.py .................... [ 1%] 1456s ................ [ 1%] 1456s testsuite/MDAnalysisTests/analysis/test_data.py . [ 1%] 1456s testsuite/MDAnalysisTests/analysis/test_density.py ..................... [ 1%] 1462s ...................... [ 1%] 1463s testsuite/MDAnalysisTests/analysis/test_dielectric.py ...... [ 1%] 1468s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py ........... [ 1%] 1475s testsuite/MDAnalysisTests/analysis/test_dihedrals.py FFF.F.....FFF.F.... [ 1%] 1481s .....FFF............... [ 1%] 1487s testsuite/MDAnalysisTests/analysis/test_distances.py ............ [ 1%] 1489s testsuite/MDAnalysisTests/analysis/test_dssp.py FFFFFFFFFFFFFFFFFFFFFFFF [ 1%] 1496s FFFFFFFFFFFFFFFFFFFFFFFFFFFFF........................................... [ 2%] 1499s ................ [ 2%] 1529s testsuite/MDAnalysisTests/analysis/test_encore.py ..F...............X..X [ 2%] 1548s ...................................... [ 2%] 1561s testsuite/MDAnalysisTests/analysis/test_gnm.py FFFF...... [ 2%] 1561s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py .............. [ 2%] 1562s ................................ [ 2%] 1562s testsuite/MDAnalysisTests/analysis/test_hole2.py s [ 2%] 1563s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [ 2%] 1563s ......... [ 2%] 1563s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [ 2%] 1564s ................. [ 3%] 1565s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py EEEEEE [ 3%] 1567s EEEEFEEEEEFFFFEEEEEFEEEF............................................ [ 3%] 1569s testsuite/MDAnalysisTests/analysis/test_leaflet.py s............ [ 3%] 1569s testsuite/MDAnalysisTests/analysis/test_lineardensity.py ........ [ 3%] 1571s testsuite/MDAnalysisTests/analysis/test_msd.py .......................ss [ 3%] 1571s sssssssssssssssssssssssssssss [ 3%] 1572s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [ 3%] 1572s [ 3%] 1573s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py .................... [ 3%] 1573s .............. [ 4%] 1575s testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [ 4%] 1576s ......................... [ 4%] 1579s testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [ 4%] 1579s ....... [ 4%] 1579s testsuite/MDAnalysisTests/analysis/test_psa.py s [ 4%] 1579s testsuite/MDAnalysisTests/analysis/test_rdf.py .................... [ 4%] 1580s testsuite/MDAnalysisTests/analysis/test_rdf_s.py ..................... [ 4%] 1581s testsuite/MDAnalysisTests/analysis/test_results.py ..................... [ 4%] 1581s ........................................................................ [ 5%] 1581s ............................................... [ 5%] 1584s testsuite/MDAnalysisTests/analysis/test_rms.py .............FFFFFFFFFFFF [ 5%] 1589s FFF................................ [ 5%] 1589s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py s [ 5%] 1589s testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [ 5%] 1590s ........................... [ 5%] 1590s testsuite/MDAnalysisTests/auxiliary/test_core.py ..... [ 5%] 1590s testsuite/MDAnalysisTests/auxiliary/test_edr.py .sssssssssssssssssssssss [ 6%] 1590s ssssssssssssssssssssssssssssssssssssssssssss [ 6%] 1590s testsuite/MDAnalysisTests/auxiliary/test_xvg.py ........................ [ 6%] 1590s ........................................................................ [ 6%] 1590s .... [ 6%] 1590s testsuite/MDAnalysisTests/converters/test_base.py .. [ 6%] 1590s testsuite/MDAnalysisTests/converters/test_rdkit.py .ssssssssssssssssssss [ 6%] 1590s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 7%] 1590s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 7%] 1590s ssssssssssssssssssssssssssssss [ 7%] 1590s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ... [ 7%] 1594s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [ 7%] 1604s ........................................................ [ 8%] 1605s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [ 8%] 1612s ...............................................................ss.ss.s.s [ 8%] 1621s s.sss....ss...s.ssss.ss.s.ss.sss....ss...s.ssss.ss.s.ss.sss....ss.s.ssss [ 8%] 1626s .......................................................s [ 9%] 1627s testsuite/MDAnalysisTests/coordinates/test_crd.py .............. [ 9%] 1627s testsuite/MDAnalysisTests/coordinates/test_dcd.py ...................... [ 9%] 1629s .......x.......ss....................................................... [ 9%] 1632s ..........................................s [ 10%] 1632s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [ 10%] 1632s .................................... [ 10%] 1633s testsuite/MDAnalysisTests/coordinates/test_dms.py ......... [ 10%] 1633s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [ 10%] 1633s ....... [ 10%] 1633s testsuite/MDAnalysisTests/coordinates/test_gms.py .................. [ 10%] 1634s testsuite/MDAnalysisTests/coordinates/test_gro.py ...................... [ 10%] 1636s .......................sss.............................................. [ 11%] 1636s ..............sss...................................................sss. [ 11%] 1655s ..................................................sss................... [ 11%] 1666s .................... [ 11%] 1666s testsuite/MDAnalysisTests/coordinates/test_gsd.py ss.... [ 11%] 1666s testsuite/MDAnalysisTests/coordinates/test_h5md.py ..................... [ 12%] 1672s ..............ss........................................................ [ 12%] 1688s .......x..................................................... [ 12%] 1688s testsuite/MDAnalysisTests/coordinates/test_lammps.py ................... [ 12%] 1697s ........................................................................ [ 13%] 1730s ................................................................. [ 13%] 1733s testsuite/MDAnalysisTests/coordinates/test_memory.py ................... [ 13%] 1743s ........x......xxx...................................................... [ 13%] 1743s .......................... [ 14%] 1743s testsuite/MDAnalysisTests/coordinates/test_mmtf.py ............ [ 14%] 1744s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 14%] 1744s [ 14%] 1745s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 14%] 1745s ..... [ 14%] 1745s testsuite/MDAnalysisTests/coordinates/test_netcdf.py ................... [ 14%] 1748s ........................................................................ [ 14%] 1751s ........................................................................ [ 15%] 1752s .................. [ 15%] 1752s testsuite/MDAnalysisTests/coordinates/test_null.py . [ 15%] 1753s testsuite/MDAnalysisTests/coordinates/test_pdb.py ...................... [ 15%] 1776s ........................................................................ [ 15%] 1780s ........................................................................ [ 16%] 1781s ................ [ 16%] 1781s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py ............... [ 16%] 1782s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 16%] 1783s ........ [ 16%] 1783s testsuite/MDAnalysisTests/coordinates/test_reader_api.py ............... [ 16%] 1783s ........................................................................ [ 16%] 1783s ........................................................................ [ 17%] 1783s ............................. [ 17%] 1783s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py ............. [ 17%] 1783s ........................................................................ [ 17%] 1786s ........................................................................ [ 18%] 1788s ................. [ 18%] 1788s testsuite/MDAnalysisTests/coordinates/test_tng.py ..ssssssssssssssssssss [ 18%] 1788s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 18%] 1788s s [ 18%] 1788s testsuite/MDAnalysisTests/coordinates/test_trc.py ...................... [ 18%] 1788s .......... [ 18%] 1788s testsuite/MDAnalysisTests/coordinates/test_trj.py ...................... [ 19%] 1789s .............. [ 19%] 1791s testsuite/MDAnalysisTests/coordinates/test_trz.py ...................... [ 19%] 1791s .. [ 19%] 1791s testsuite/MDAnalysisTests/coordinates/test_txyz.py ...... [ 19%] 1791s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 19%] 1792s ........................................................... [ 19%] 1792s testsuite/MDAnalysisTests/coordinates/test_writer_api.py .ss............ [ 19%] 1792s ......ss.....s............ss.....s........... [ 19%] 1792s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py .... [ 19%] 1794s testsuite/MDAnalysisTests/coordinates/test_xdr.py ...................... [ 20%] 1804s ........................................................................ [ 20%] 1805s ....ss.................................................................. [ 20%] 1806s .ss......................................................... [ 21%] 1806s testsuite/MDAnalysisTests/coordinates/test_xyz.py ...................... [ 21%] 1806s ...............ss....................................................... [ 21%] 1807s .................ss....................................... [ 21%] 1807s testsuite/MDAnalysisTests/core/test_accessors.py ssss..s [ 21%] 1808s testsuite/MDAnalysisTests/core/test_accumulate.py ...................... [ 22%] 1816s ................................................................... [ 22%] 1818s testsuite/MDAnalysisTests/core/test_atom.py .................... [ 22%] 1822s testsuite/MDAnalysisTests/core/test_atomgroup.py ....................... [ 22%] 1834s ........................................................................ [ 22%] 1835s ........................................................................ [ 23%] 1847s ........................................................................ [ 23%] 1865s ........................................................................ [ 24%] 1881s ........................................................................ [ 24%] 1887s .......................................................... [ 24%] 1887s testsuite/MDAnalysisTests/core/test_atomselections.py .................. [ 24%] 1887s ........................................................................ [ 25%] 1888s ........................................................................ [ 25%] 1903s ..................sssssssssssssssssss................................... [ 25%] 1904s ........................................................................ [ 26%] 1904s ........................................................................ [ 26%] 1905s ........................................................................ [ 27%] 1915s .....................................sssss...........ssssss.... [ 27%] 1915s testsuite/MDAnalysisTests/core/test_copying.py ......................... [ 27%] 1916s .................... [ 27%] 1917s testsuite/MDAnalysisTests/core/test_fragments.py ................ [ 27%] 1917s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%] 1920s ................................................. [ 27%] 1920s testsuite/MDAnalysisTests/core/test_groups.py .......................... [ 28%] 1920s ........................................................................ [ 28%] 1920s ........................................................................ [ 28%] 1920s ........................................................................ [ 29%] 1922s ........................................................................ [ 29%] 1922s ........................................................................ [ 29%] 1922s ........................................................................ [ 30%] 1922s ........................................................................ [ 30%] 1942s ....................................................................... [ 31%] 1942s testsuite/MDAnalysisTests/core/test_index_dtype.py ............... [ 31%] 1942s testsuite/MDAnalysisTests/core/test_requires.py .... [ 31%] 1942s testsuite/MDAnalysisTests/core/test_residue.py .... [ 31%] 1944s testsuite/MDAnalysisTests/core/test_residuegroup.py s..................s [ 31%] 1945s ssss..... [ 31%] 1945s testsuite/MDAnalysisTests/core/test_segment.py ....... [ 31%] 1946s testsuite/MDAnalysisTests/core/test_segmentgroup.py ........... [ 31%] 1946s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%] 1946s ........................................ [ 31%] 1947s testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%] 1947s ...................................................................x.... [ 32%] 1948s ........................................................ [ 32%] 1948s testsuite/MDAnalysisTests/core/test_topologyobjects.py ................. [ 32%] 1951s ...................................................................... [ 32%] 1953s testsuite/MDAnalysisTests/core/test_universe.py .................sssssss [ 33%] 1958s s....................................................................... [ 33%] 1961s ........................................................................ [ 33%] 1965s ........................................................................ [ 34%] 1967s .................................... [ 34%] 1967s testsuite/MDAnalysisTests/core/test_unwrap.py .......................... [ 34%] 1968s ........................................................................ [ 34%] 1968s ........................................................................ [ 35%] 1969s ........................................................................ [ 35%] 1969s ........................................................................ [ 35%] 1969s ........................................................................ [ 36%] 1969s ........................................................................ [ 36%] 1970s ................................................... [ 36%] 1973s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py .............. [ 36%] 1973s . [ 36%] 1973s testsuite/MDAnalysisTests/core/test_wrap.py ............................ [ 37%] 1973s ........................................................................ [ 37%] 1974s ........................................................................ [ 37%] 1974s ........................................................................ [ 38%] 1974s ........................................................................ [ 38%] 1975s ........................................................................ [ 38%] 1975s ........................................................................ [ 39%] 1976s ......................................................... [ 39%] 1976s testsuite/MDAnalysisTests/formats/test_libdcd.py ....................... [ 39%] 1978s ........................................................................ [ 40%] 1978s ...... [ 40%] 1978s testsuite/MDAnalysisTests/formats/test_libmdaxdr.py .................... [ 40%] 1978s ........................................................................ [ 40%] 1978s ... [ 40%] 2014s testsuite/MDAnalysisTests/guesser/test_base.py ........................ [ 40%] 2014s testsuite/MDAnalysisTests/guesser/test_default_guesser.py .............. [ 40%] 2015s ...........................sssssssssss [ 40%] 2015s testsuite/MDAnalysisTests/import/test_import.py .. [ 40%] 2015s testsuite/MDAnalysisTests/lib/test_augment.py .......................... [ 41%] 2015s .......... [ 41%] 2015s testsuite/MDAnalysisTests/lib/test_cutil.py ............. [ 41%] 2015s testsuite/MDAnalysisTests/lib/test_distances.py ........................ [ 41%] 2016s ........................................................................ [ 41%] 2016s ........................................................................ [ 42%] 2016s ........................................................................ [ 42%] 2016s ........................................................................ [ 42%] 2016s ........................................................................ [ 43%] 2017s ........................................................................ [ 43%] 2024s ........................................................................ [ 43%] 2027s ........................................................................ [ 44%] 2027s ........................................................................ [ 44%] 2027s ........................................................................ [ 45%] 2028s ........................................................................ [ 45%] 2028s ........................................................................ [ 45%] 2028s ........................................................................ [ 46%] 2028s ........................................................................ [ 46%] 2029s ........................................................................ [ 46%] 2029s ........................................................................ [ 47%] 2029s ........................................................................ [ 47%] 2029s ........................................................................ [ 47%] 2029s ........................................................................ [ 48%] 2029s ........................................................................ [ 48%] 2029s ........................................................................ [ 49%] 2029s ........................................................................ [ 49%] 2029s ........................................................................ [ 49%] 2030s ........................................................................ [ 50%] 2030s ........................................................................ [ 50%] 2030s ........................................................................ [ 50%] 2030s ........................................................................ [ 51%] 2030s ........................................................................ [ 51%] 2030s ........................................................................ [ 51%] 2030s ........................................................................ [ 52%] 2030s ........................................................................ [ 52%] 2031s ........................................................................ [ 53%] 2031s ........................................................................ [ 53%] 2031s ........................................................................ [ 53%] 2031s ............................................... [ 54%] 2031s testsuite/MDAnalysisTests/lib/test_log.py ... [ 54%] 2031s testsuite/MDAnalysisTests/lib/test_neighborsearch.py .. [ 54%] 2036s testsuite/MDAnalysisTests/lib/test_nsgrid.py ........................... [ 54%] 2037s ..s [ 54%] 2037s testsuite/MDAnalysisTests/lib/test_pkdtree.py ................. [ 54%] 2037s testsuite/MDAnalysisTests/lib/test_qcprot.py .... [ 54%] 2037s testsuite/MDAnalysisTests/lib/test_util.py ............................. [ 54%] 2037s ........................................................................ [ 54%] 2037s ........................................................................ [ 55%] 2037s ........................................................................ [ 55%] 2038s ........................................................................ [ 55%] 2038s ........................................................................ [ 56%] 2038s ........................................................................ [ 56%] 2038s ........................................................................ [ 57%] 2038s ........................................................................ [ 57%] 2038s ........................................................................ [ 57%] 2038s ........................................................................ [ 58%] 2038s ........................................................................ [ 58%] 2038s ........................................................................ [ 58%] 2038s ........................................................................ [ 59%] 2038s ........................................................................ [ 59%] 2039s ........................................................................ [ 59%] 2039s ........................................................................ [ 60%] 2039s ........................................................................ [ 60%] 2039s ........................................................................ [ 61%] 2039s ........................................................................ [ 61%] 2039s ........................................................................ [ 61%] 2039s ........................................................................ [ 62%] 2039s ........................................................................ [ 62%] 2039s ........................................................................ [ 62%] 2039s ........................................................................ [ 63%] 2040s ........................................................................ [ 63%] 2040s ........................................................................ [ 63%] 2040s ........................................................................ [ 64%] 2040s ........................................................................ [ 64%] 2040s ........................................................................ [ 65%] 2040s ........................................................................ [ 65%] 2040s ........................................................................ [ 65%] 2040s ........................................................................ [ 66%] 2040s ........................................................................ [ 66%] 2041s ........................................................................ [ 66%] 2041s ........................................................................ [ 67%] 2041s ........................................................................ [ 67%] 2041s ........................................................................ [ 68%] 2041s ........................................................................ [ 68%] 2041s ........................................................................ [ 68%] 2041s ........................................................................ [ 69%] 2041s ........................................................................ [ 69%] 2041s ........................................................................ [ 69%] 2042s ........................................................................ [ 70%] 2042s ........................................................................ [ 70%] 2042s ........................................................................ [ 70%] 2042s ........................................................................ [ 71%] 2042s ........................................................................ [ 71%] 2042s ........................................................................ [ 72%] 2042s ........................................................................ [ 72%] 2042s ........................................................................ [ 72%] 2042s ........................................................................ [ 73%] 2042s ........................................................................ [ 73%] 2042s ........................................................................ [ 73%] 2043s ........................................................................ [ 74%] 2043s ........................................................................ [ 74%] 2043s ........................................................................ [ 74%] 2043s ........................................................................ [ 75%] 2043s ........................................................................ [ 75%] 2043s ........................................................................ [ 76%] 2043s ........................................................................ [ 76%] 2043s ........................................................................ [ 76%] 2043s ........................................................................ [ 77%] 2043s ........................................................................ [ 77%] 2043s ........................................................................ [ 77%] 2043s ........................................................................ [ 78%] 2044s ........................................................................ [ 78%] 2044s ........................................................................ [ 79%] 2044s ........................................................................ [ 79%] 2044s ........................................................................ [ 79%] 2044s ........................................................................ [ 80%] 2044s ........................................................................ [ 80%] 2045s ........................................................................ [ 80%] 2045s ........................................................................ [ 81%] 2045s ........................................................................ [ 81%] 2045s ........................................................................ [ 81%] 2045s ........................................................................ [ 82%] 2045s ........................................................................ [ 82%] 2045s ........................................................................ [ 83%] 2045s ........................................................................ [ 83%] 2046s .........................................s.............................. [ 83%] 2046s ........................................................................ [ 84%] 2047s .............s.......................................................... [ 84%] 2053s ........................................................................ [ 84%] 2053s ..................................................... [ 85%] 2054s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py FFFFFFFFFF [ 85%] 2067s FFFFFFF................................ [ 85%] 2068s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py .... [ 85%] 2068s .... [ 85%] 2068s testsuite/MDAnalysisTests/test_api.py ................................. [ 85%] 2073s testsuite/MDAnalysisTests/topology/test_altloc.py ... [ 85%] 2074s testsuite/MDAnalysisTests/topology/test_crd.py .......... [ 85%] 2074s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 85%] 2074s .............................................. [ 86%] 2075s testsuite/MDAnalysisTests/topology/test_dms.py ...................... [ 86%] 2075s testsuite/MDAnalysisTests/topology/test_fhiaims.py ............ [ 86%] 2075s testsuite/MDAnalysisTests/topology/test_gms.py ......................... [ 86%] 2075s ......... [ 86%] 2078s testsuite/MDAnalysisTests/topology/test_gro.py ................. [ 86%] 2078s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%] 2078s ...... [ 86%] 2078s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 86%] 2078s ..............ssssssssss..........s [ 86%] 2079s testsuite/MDAnalysisTests/topology/test_hoomdxml.py .................. [ 86%] 2079s testsuite/MDAnalysisTests/topology/test_itp.py ......................... [ 87%] 2079s ........................................................................ [ 87%] 2080s ......................................... [ 87%] 2084s testsuite/MDAnalysisTests/topology/test_lammpsdata.py .................. [ 87%] 2084s ........................................................................ [ 88%] 2085s ........................................................... [ 88%] 2085s testsuite/MDAnalysisTests/topology/test_minimal.py ..................... [ 88%] 2085s ........... [ 88%] 2085s testsuite/MDAnalysisTests/topology/test_mmtf.py ........................ [ 88%] 2086s .............................................. [ 88%] 2086s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%] 2086s ........ [ 89%] 2089s testsuite/MDAnalysisTests/topology/test_pdb.py ......................... [ 89%] 2090s ........................... [ 89%] 2090s testsuite/MDAnalysisTests/topology/test_pdbqt.py .......... [ 89%] 2090s testsuite/MDAnalysisTests/topology/test_pqr.py ........................ [ 89%] 2096s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%] 2099s ........................................ [ 89%] 2099s testsuite/MDAnalysisTests/topology/test_tables.py . [ 89%] 2100s testsuite/MDAnalysisTests/topology/test_top.py ......................... [ 90%] 2105s ........................................................................ [ 90%] 2105s ........................................................................ [ 90%] 2105s ........... [ 90%] 2105s testsuite/MDAnalysisTests/topology/test_topology_base.py ... [ 90%] 2106s testsuite/MDAnalysisTests/topology/test_topology_str_types.py .......... [ 90%] 2112s ........................................................................ [ 91%] 2114s .................. [ 91%] 2119s testsuite/MDAnalysisTests/topology/test_tprparser.py ................... [ 91%] 2126s ........................................................................ [ 91%] 2134s ........................................................................ [ 92%] 2141s ........................................................................ [ 92%] 2148s ........................................................................ [ 92%] 2157s ........................................................................ [ 93%] 2157s ........................................................................ [ 93%] 2157s ........................................................................ [ 93%] 2157s ........................................................................ [ 94%] 2157s ........................................................................ [ 94%] 2158s ........................................................................ [ 95%] 2158s ........................................................................ [ 95%] 2159s ........................................................................ [ 95%] 2161s .................................... [ 95%] 2161s testsuite/MDAnalysisTests/topology/test_txyz.py ....................... [ 96%] 2161s testsuite/MDAnalysisTests/topology/test_xpdb.py .......... [ 96%] 2162s testsuite/MDAnalysisTests/topology/test_xyz.py ......................... [ 96%] 2162s ... [ 96%] 2162s testsuite/MDAnalysisTests/transformations/test_base.py ..... [ 96%] 2162s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%] 2162s ...... [ 96%] 2162s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%] 2162s ......................................... [ 96%] 2163s testsuite/MDAnalysisTests/transformations/test_nojump.py ............ [ 96%] 2163s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%] 2163s . [ 96%] 2164s testsuite/MDAnalysisTests/transformations/test_rotate.py ............... [ 96%] 2164s ............................ [ 97%] 2164s testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%] 2164s ............ [ 97%] 2172s testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%] 2172s ....... [ 97%] 2172s testsuite/MDAnalysisTests/utils/test_authors.py . [ 97%] 2172s testsuite/MDAnalysisTests/utils/test_datafiles.py .... [ 97%] 2172s testsuite/MDAnalysisTests/utils/test_duecredit.py ........... [ 97%] 2172s testsuite/MDAnalysisTests/utils/test_failure.py . [ 97%] 2172s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%] 2172s ........................................................................ [ 97%] 2172s ........................................................................ [ 98%] 2172s ............................................. [ 98%] 2172s testsuite/MDAnalysisTests/utils/test_log.py . [ 98%] 2172s testsuite/MDAnalysisTests/utils/test_meta.py .... [ 98%] 2173s testsuite/MDAnalysisTests/utils/test_modelling.py ............. [ 98%] 2174s testsuite/MDAnalysisTests/utils/test_persistence.py ....... [ 98%] 2185s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%] 2185s ..............ss.. [ 98%] 2185s testsuite/MDAnalysisTests/utils/test_qcprot.py ...... [ 98%] 2187s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%] 2187s [ 98%] 2187s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 99%] 2188s ............... [ 99%] 2188s testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%] 2188s ........................................................................ [ 99%] 2188s ........................................................ [ 99%] 2188s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%] 2188s ....... [ 99%] 2188s testsuite/MDAnalysisTests/visualization/test_streamlines.py FFF [100%] 2188s 2188s ==================================== ERRORS ==================================== 2188s _______ ERROR at setup of TestBAT.test_bat_number_of_frames[client_BAT0] _______ 2188s 2188s self = 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture() 2188s def bat(self, selected_residues, client_BAT): 2188s R = BAT(selected_residues) 2188s > R.run(**client_BAT) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:46: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _________ ERROR at setup of TestBAT.test_bat_coordinates[client_BAT0] __________ 2188s 2188s self = 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture() 2188s def bat(self, selected_residues, client_BAT): 2188s R = BAT(selected_residues) 2188s > R.run(**client_BAT) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:46: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ________ ERROR at setup of TestBAT.test_bat_reconstruction[client_BAT0] ________ 2188s 2188s self = 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture() 2188s def bat(self, selected_residues, client_BAT): 2188s R = BAT(selected_residues) 2188s > R.run(**client_BAT) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:46: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ______________ ERROR at setup of TestBAT.test_bat_IO[client_BAT0] ______________ 2188s 2188s self = 2188s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_bat_IO_client_BAT0_0') 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture 2188s def bat_npz(self, tmpdir, selected_residues, client_BAT): 2188s filename = str(tmpdir / 'test_bat_IO.npy') 2188s R = BAT(selected_residues) 2188s > R.run(**client_BAT) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:53: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ________ ERROR at setup of TestBAT.test_bat_incorrect_dims[client_BAT0] ________ 2188s 2188s self = 2188s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_bat_incorrect_dims_client0') 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture 2188s def bat_npz(self, tmpdir, selected_residues, client_BAT): 2188s filename = str(tmpdir / 'test_bat_IO.npy') 2188s R = BAT(selected_residues) 2188s > R.run(**client_BAT) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:53: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestBAT.test_Cartesian_does_not_modify_input[client_BAT0] __ 2188s 2188s self = 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture() 2188s def bat(self, selected_residues, client_BAT): 2188s R = BAT(selected_residues) 2188s > R.run(**client_BAT) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:46: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P.test_hbond_analysis[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P.test_count_by_time[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P.test_count_by_type[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P.test_count_by_ids[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P.test_hbonds_deprecated_attr[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisIdeal.test_count_by_type[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisIdeal.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:189: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisIdeal.test_first_hbond[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisIdeal.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:189: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisIdeal.test_count_by_time[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisIdeal.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:189: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisIdeal.test_hydrogen_bond_lifetime[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisIdeal.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:189: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisIdeal.test_hydrogen_bond_lifetime_intermittency[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisIdeal.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:189: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisNoRes.test_count_by_type[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisNoRes.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:354: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisNoRes.test_first_hbond[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisNoRes.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:354: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisNoRes.test_count_by_time[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisNoRes.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:354: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisNoRes.test_hydrogen_bond_lifetime[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisNoRes.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:354: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisNoRes.test_hydrogen_bond_lifetime_intermittency[client_HydrogenBondAnalysis0] _ 2188s 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @staticmethod 2188s @pytest.fixture(scope='class') 2188s def hydrogen_bonds(universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis( 2188s universe, 2188s **TestHydrogenBondAnalysisNoRes.kwargs 2188s ) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:354: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_.test_hbond_analysis[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_.test_count_by_time[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_.test_count_by_type[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_.test_count_by_ids[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_.test_hbonds_deprecated_attr[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:58: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3PStartStep.test_hbond_analysis[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis, start=1, step=2) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:638: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3PStartStep.test_count_by_time[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis, start=1, step=2) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:638: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ ERROR at setup of TestHydrogenBondAnalysisTIP3PStartStep.test_count_by_type[client_HydrogenBondAnalysis0] _ 2188s 2188s self = 2188s universe = 2188s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.fixture(scope='class') 2188s def h(self, universe, client_HydrogenBondAnalysis): 2188s h = HydrogenBondAnalysis(universe, **self.kwargs) 2188s > h.run(**client_HydrogenBondAnalysis, start=1, step=2) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:638: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s =================================== FAILURES =================================== 2188s ____ test_AnalysisFromFunction[client_AnalysisFromFunction0-None-None-2-49] ____ 2188s 2188s u = , start = None, stop = None, step = 2 2188s nframes = 49 2188s client_AnalysisFromFunction = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.mark.parametrize('start, stop, step, nframes', [ 2188s (None, None, 2, 49), 2188s (None, 50, 2, 25), 2188s (20, 50, 2, 15), 2188s (20, 50, None, 30) 2188s ]) 2188s def test_AnalysisFromFunction(u, start, stop, step, nframes, client_AnalysisFromFunction): 2188s # client_AnalysisFromFunction is defined [here](testsuite/MDAnalysisTests/analysis/conftest.py), 2188s # and determines a set of parameters ('backend', 'n_workers'), taking only backends 2188s # that are implemented for a given subclass, to run the test against. 2188s ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms) 2188s ana1.run(start=start, stop=stop, step=step, **client_AnalysisFromFunction) 2188s 2188s ana2 = base.AnalysisFromFunction(simple_function, u.atoms) 2188s ana2.run(start=start, stop=stop, step=step, **client_AnalysisFromFunction) 2188s 2188s ana3 = base.AnalysisFromFunction(simple_function, u.trajectory, u.atoms) 2188s > ana3.run(start=start, stop=stop, step=step, **client_AnalysisFromFunction) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_base.py:439: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s /usr/lib/python3.13/multiprocessing/process.py:121: in start 2188s self._popen = self._Popen(self) 2188s /usr/lib/python3.13/multiprocessing/context.py:282: in _Popen 2188s return Popen(process_obj) 2188s /usr/lib/python3.13/multiprocessing/popen_fork.py:20: in __init__ 2188s self._launch(process_obj) 2188s /usr/lib/python3.13/multiprocessing/popen_fork.py:76: in _launch 2188s atexit._run_exitfuncs() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s n = 15 2188s f = 2188s 2188s > signal.signal(signal.SIGTERM, lambda n, f: sys.exit(1)) 2188s E SystemExit: 1 2188s 2188s /usr/lib/python3/dist-packages/gsd/__init__.py:25: SystemExit 2188s _____ test_AnalysisFromFunction[client_AnalysisFromFunction0-None-50-2-25] _____ 2188s 2188s u = , start = None, stop = 50, step = 2, nframes = 25 2188s client_AnalysisFromFunction = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.mark.parametrize('start, stop, step, nframes', [ 2188s (None, None, 2, 49), 2188s (None, 50, 2, 25), 2188s (20, 50, 2, 15), 2188s (20, 50, None, 30) 2188s ]) 2188s def test_AnalysisFromFunction(u, start, stop, step, nframes, client_AnalysisFromFunction): 2188s # client_AnalysisFromFunction is defined [here](testsuite/MDAnalysisTests/analysis/conftest.py), 2188s # and determines a set of parameters ('backend', 'n_workers'), taking only backends 2188s # that are implemented for a given subclass, to run the test against. 2188s ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms) 2188s > ana1.run(start=start, stop=stop, step=step, **client_AnalysisFromFunction) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_base.py:433: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ______ test_AnalysisFromFunction[client_AnalysisFromFunction0-20-50-2-15] ______ 2188s 2188s u = , start = 20, stop = 50, step = 2, nframes = 15 2188s client_AnalysisFromFunction = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.mark.parametrize('start, stop, step, nframes', [ 2188s (None, None, 2, 49), 2188s (None, 50, 2, 25), 2188s (20, 50, 2, 15), 2188s (20, 50, None, 30) 2188s ]) 2188s def test_AnalysisFromFunction(u, start, stop, step, nframes, client_AnalysisFromFunction): 2188s # client_AnalysisFromFunction is defined [here](testsuite/MDAnalysisTests/analysis/conftest.py), 2188s # and determines a set of parameters ('backend', 'n_workers'), taking only backends 2188s # that are implemented for a given subclass, to run the test against. 2188s ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms) 2188s > ana1.run(start=start, stop=stop, step=step, **client_AnalysisFromFunction) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_base.py:433: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ____ test_AnalysisFromFunction[client_AnalysisFromFunction0-20-50-None-30] _____ 2188s 2188s u = , start = 20, stop = 50, step = None, nframes = 30 2188s client_AnalysisFromFunction = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s @pytest.mark.parametrize('start, stop, step, nframes', [ 2188s (None, None, 2, 49), 2188s (None, 50, 2, 25), 2188s (20, 50, 2, 15), 2188s (20, 50, None, 30) 2188s ]) 2188s def test_AnalysisFromFunction(u, start, stop, step, nframes, client_AnalysisFromFunction): 2188s # client_AnalysisFromFunction is defined [here](testsuite/MDAnalysisTests/analysis/conftest.py), 2188s # and determines a set of parameters ('backend', 'n_workers'), taking only backends 2188s # that are implemented for a given subclass, to run the test against. 2188s ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms) 2188s > ana1.run(start=start, stop=stop, step=step, **client_AnalysisFromFunction) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_base.py:433: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _____ test_AnalysisFromFunction_args_content[client_AnalysisFromFunction0] _____ 2188s 2188s u = 2188s client_AnalysisFromFunction = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_AnalysisFromFunction_args_content(u, client_AnalysisFromFunction): 2188s protein = u.select_atoms('protein') 2188s masses = protein.masses.reshape(-1, 1) 2188s another = mda.Universe(TPR, XTC).select_atoms("protein") 2188s ans = base.AnalysisFromFunction(mass_xyz, protein, another, masses) 2188s assert len(ans.args) == 3 2188s > result = np.sum(ans.run(**client_AnalysisFromFunction).results.timeseries) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_base.py:472: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ____________ TestBAT.test_bat_coordinates_single_frame[client_BAT0] ____________ 2188s 2188s self = 2188s selected_residues = 2188s client_BAT = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_bat_coordinates_single_frame(self, selected_residues, client_BAT): 2188s > bat = BAT(selected_residues).run(start=1, stop=2, **client_BAT).results.bat 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_bat.py:77: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _________________ TestDihedral.test_dihedral[client_Dihedral0] _________________ 2188s 2188s self = 2188s atomgroup = 2188s client_Dihedral = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_dihedral(self, atomgroup, client_Dihedral): 2188s # client_Dihedral is defined in testsuite/analysis/conftest.py 2188s # among with other testing fixtures. During testing, it will 2188s # collect all possible backends and reasonable number of workers 2188s # for a given AnalysisBase subclass, and extend the tests 2188s # to run with all of them. 2188s 2188s > dihedral = Dihedral([atomgroup]).run(**client_Dihedral) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:53: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s __________ TestDihedral.test_dihedral_single_frame[client_Dihedral0] ___________ 2188s 2188s self = 2188s atomgroup = 2188s client_Dihedral = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_dihedral_single_frame(self, atomgroup, client_Dihedral): 2188s > dihedral = Dihedral([atomgroup]).run(start=5, stop=6, **client_Dihedral) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:61: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ______________ TestDihedral.test_atomgroup_list[client_Dihedral0] ______________ 2188s 2188s self = 2188s atomgroup = 2188s client_Dihedral = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_atomgroup_list(self, atomgroup, client_Dihedral): 2188s > dihedral = Dihedral([atomgroup, atomgroup]).run(**client_Dihedral) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:69: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s __________ TestDihedral.test_dihedral_attr_warning[client_Dihedral0] ___________ 2188s 2188s self = 2188s atomgroup = 2188s client_Dihedral = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_dihedral_attr_warning(self, atomgroup, client_Dihedral): 2188s > dihedral = Dihedral([atomgroup]).run(stop=2, **client_Dihedral) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:81: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ___________ TestRamachandran.test_ramachandran[client_Ramachandran0] ___________ 2188s 2188s self = 2188s universe = 2188s rama_ref_array = array([[[-124.48583372, 94.9259782 ], 2188s [ -96.37595309, 131.32777565], 2188s [ -89.19265646, 140.09586001]... [ -87.00735667, -55.19692701], 2188s [ -66.3164188 , -19.67304583], 2188s [-129.59004461, 40.81708804]]]) 2188s client_Ramachandran = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_ramachandran(self, universe, rama_ref_array, client_Ramachandran): 2188s > rama = Ramachandran(universe.select_atoms("protein")).run( 2188s **client_Ramachandran) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:99: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ____ TestRamachandran.test_ramachandran_single_frame[client_Ramachandran0] _____ 2188s 2188s self = 2188s universe = 2188s rama_ref_array = array([[[-124.48583372, 94.9259782 ], 2188s [ -96.37595309, 131.32777565], 2188s [ -89.19265646, 140.09586001]... [ -87.00735667, -55.19692701], 2188s [ -66.3164188 , -19.67304583], 2188s [-129.59004461, 40.81708804]]]) 2188s client_Ramachandran = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_ramachandran_single_frame(self, universe, rama_ref_array, client_Ramachandran): 2188s > rama = Ramachandran(universe.select_atoms("protein")).run( 2188s start=5, stop=6, **client_Ramachandran) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:107: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _ TestRamachandran.test_ramachandran_residue_selections[client_Ramachandran0] __ 2188s 2188s self = 2188s universe = 2188s client_Ramachandran = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_ramachandran_residue_selections(self, universe, client_Ramachandran): 2188s > rama = Ramachandran(universe.select_atoms("resname GLY")).run( 2188s **client_Ramachandran) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:115: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ____ TestRamachandran.test_outside_protein_unchecked[client_Ramachandran0] _____ 2188s 2188s self = 2188s universe = 2188s client_Ramachandran = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_outside_protein_unchecked(self, universe, client_Ramachandran): 2188s > rama = Ramachandran(universe.select_atoms("resid 220"), 2188s check_protein=False).run(**client_Ramachandran) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:129: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s _____________________ TestJanin.test_janin[client_Janin0] ______________________ 2188s 2188s self = 2188s universe = 2188s janin_ref_array = array([[[193.64583542, 68.93897046], 2188s [303.68602905, 177.39171502], 2188s [295.786122 , 155.79552693], 2188s ....., 2188s [303.1546012 , 187.5011965 ], 2188s [294.82576567, 162.35432983], 2188s [296.80732627, 179.67398714]]]) 2188s client_Janin = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_janin(self, universe, janin_ref_array, client_Janin): 2188s > self._test_janin(universe, janin_ref_array, client_Janin) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:171: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:178: in _test_janin 2188s janin = Janin(u.select_atoms("protein")).run(**client_Janin) 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2188s ___________________ TestJanin.test_janin_tpr[client_Janin0] ____________________ 2188s 2188s self = 2188s universe_tpr = 2188s janin_ref_array = array([[[193.64583542, 68.93897046], 2188s [303.68602905, 177.39171502], 2188s [295.786122 , 155.79552693], 2188s ....., 2188s [303.1546012 , 187.5011965 ], 2188s [294.82576567, 162.35432983], 2188s [296.80732627, 179.67398714]]]) 2188s client_Janin = {'backend': 'multiprocessing', 'n_workers': 2} 2188s 2188s def test_janin_tpr(self, universe_tpr, janin_ref_array, client_Janin): 2188s """Test that CYSH are filtered (#2898)""" 2188s > self._test_janin(universe_tpr, janin_ref_array, client_Janin) 2188s 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:175: 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:178: in _test_janin 2188s janin = Janin(u.select_atoms("protein")).run(**client_Janin) 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2188s remote_objects: list["AnalysisBase"] = executor.apply( 2188s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2188s with Pool(processes=self.n_workers) as pool: 2188s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2188s return Pool(processes, initializer, initargs, maxtasksperchild, 2188s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2188s self._repopulate_pool() 2188s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2188s return self._repopulate_pool_static(self._ctx, self.Process, 2188s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2188s w.start() 2188s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2188s 2188s self = 2188s 2188s def start(self): 2188s ''' 2188s Start child process 2188s ''' 2188s self._check_closed() 2188s assert self._popen is None, 'cannot start a process twice' 2188s assert self._parent_pid == os.getpid(), \ 2188s 'can only start a process object created by current process' 2188s > assert not _current_process._config.get('daemon'), \ 2188s 'daemonic processes are not allowed to have children' 2188s E AssertionError: daemonic processes are not allowed to have children 2188s 2188s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ____________ TestJanin.test_janin_residue_selections[client_Janin0] ____________ 2189s 2189s self = 2189s universe = 2189s client_Janin = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_janin_residue_selections(self, universe, client_Janin): 2189s > janin = Janin(universe.select_atoms("resname LYS")).run(**client_Janin) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dihedrals.py:193: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1ahsA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1ahsA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1bvyF.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1bvyF.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1dx5I.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1dx5I.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1eteA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1eteA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1h4aX.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1h4aX.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1i8nA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1i8nA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1lpbA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1lpbA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1mr1D.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1mr1D.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1or4A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1or4A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1pdoA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1pdoA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1v7mV.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1v7mV.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1y1lA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1y1lA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2a2lA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2a2lA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2cayA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2cayA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2cviA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2cviA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2fvvA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2fvvA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2gu3A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2gu3A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2i39A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2i39A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2j49A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2j49A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2qdlA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2qdlA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2va0A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2va0A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xcjA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xcjA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xr6A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xr6A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3a4rA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3a4rA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3aqgA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3aqgA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3e8mA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3e8mA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ejfA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ejfA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3fhkA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3fhkA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gfsA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gfsA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gknA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gknA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gwiA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gwiA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3hklA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3hklA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ieyB.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ieyB.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ii2A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ii2A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3k7pA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3k7pA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3l4rA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3l4rA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3lqcA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3lqcA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nbkA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nbkA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nngA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nngA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ny7A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ny7A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nzmA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nzmA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3on9A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3on9A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3pivA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3pivA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3q4oA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3q4oA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3so6A.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3so6A.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3t5gB.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3t5gB.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3vjzA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3vjzA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/4dkcA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/4dkcA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/4gcnA.pdb.gz] _ 2189s 2189s pdb_filename = '/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/4gcnA.pdb.gz' 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s @pytest.mark.parametrize("pdb_filename", glob.glob(f"{DSSP_FOLDER}/?????.pdb.gz")) 2189s def test_file_guess_hydrogens(pdb_filename, client_DSSP): 2189s u = mda.Universe(pdb_filename) 2189s with open(f"{pdb_filename.rstrip('.gz')}.dssp", "r") as fin: 2189s correct_answ = fin.read().strip().split()[0] 2189s 2189s > run = DSSP(u, guess_hydrogens=True).run(**client_DSSP) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:18: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________________________ test_trajectory[client_DSSP0] _________________________ 2189s 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_trajectory(client_DSSP): 2189s u = mda.Universe(TPR, XTC).select_atoms("protein").universe 2189s > run = DSSP(u).run(**client_DSSP, stop=10) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:25: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _________________________ test_atomgroup[client_DSSP0] _________________________ 2189s 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_atomgroup(client_DSSP): 2189s protein = mda.Universe(TPR, XTC).select_atoms("protein") 2189s > run = DSSP(protein).run(**client_DSSP, stop=10) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:37: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _________________ test_trajectory_with_hydrogens[client_DSSP0] _________________ 2189s 2189s client_DSSP = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_trajectory_with_hydrogens(client_DSSP): 2189s u = mda.Universe(TPR, XTC).select_atoms("protein").universe 2189s > run = DSSP(u, guess_hydrogens=False).run(**client_DSSP, stop=10) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_dssp.py:47: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _____________________ TestEncore.test_parallel_calculation _____________________ 2189s 2189s self = 2189s 2189s @pytest.mark.xfail(os.name == 'nt', 2189s reason="Not yet supported on Windows.") 2189s def test_parallel_calculation(self): 2189s 2189s arguments = [tuple([i]) for i in np.arange(0,100)] 2189s 2189s parallel_calculation = encore.utils.ParallelCalculation(function=function, 2189s n_jobs=4, 2189s args=arguments) 2189s > results = parallel_calculation.run() 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_encore.py:139: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/encore/utils.py:300: in run 2189s manager = Manager() 2189s /usr/lib/python3.13/multiprocessing/context.py:57: in Manager 2189s m.start() 2189s /usr/lib/python3.13/multiprocessing/managers.py:565: in start 2189s self._process.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________________________ test_gnm[client_GNMAnalysis0] _________________________ 2189s 2189s universe = 2189s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_gnm_client_GNMAnalysis0_0') 2189s client_GNMAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_gnm(universe, tmpdir, client_GNMAnalysis): 2189s output = os.path.join(str(tmpdir), 'output.txt') 2189s gnm = mda.analysis.gnm.GNMAnalysis(universe, ReportVector=output) 2189s > gnm.run(**client_GNMAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_gnm.py:44: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ____________________ test_gnm_run_step[client_GNMAnalysis0] ____________________ 2189s 2189s universe = 2189s client_GNMAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_gnm_run_step(universe, client_GNMAnalysis): 2189s gnm = mda.analysis.gnm.GNMAnalysis(universe) 2189s > gnm.run(step=3, **client_GNMAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_gnm.py:56: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ______________ test_closeContactGNMAnalysis[client_GNMAnalysis0] _______________ 2189s 2189s universe = 2189s client_GNMAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_closeContactGNMAnalysis(universe, client_GNMAnalysis): 2189s gnm = mda.analysis.gnm.closeContactGNMAnalysis(universe, weights="size") 2189s > gnm.run(stop=2, **client_GNMAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_gnm.py:93: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________ test_closeContactGNMAnalysis_weights_None[client_GNMAnalysis0] ________ 2189s 2189s universe = 2189s client_GNMAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis): 2189s gnm = mda.analysis.gnm.closeContactGNMAnalysis(universe, weights=None) 2189s > gnm.run(stop=2, **client_GNMAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_gnm.py:119: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisIdeal.test_logging_step_not_1[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s caplog = <_pytest.logging.LogCaptureFixture object at 0xc6a2f988> 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_logging_step_not_1(self, universe, caplog, 2189s client_HydrogenBondAnalysis): 2189s hbonds = HydrogenBondAnalysis(universe, **self.kwargs) 2189s # using step 2 2189s > hbonds.run(**client_HydrogenBondAnalysis, step=2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:273: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisNoRes.test_logging_step_not_1[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s caplog = <_pytest.logging.LogCaptureFixture object at 0xc4d5e870> 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_logging_step_not_1(self, universe, caplog, 2189s client_HydrogenBondAnalysis): 2189s hbonds = HydrogenBondAnalysis(universe, **self.kwargs) 2189s # using step 2 2189s > hbonds.run(**client_HydrogenBondAnalysis, step=2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:273: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisBetween.test_between_all[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_between_all(self, universe, client_HydrogenBondAnalysis): 2189s # don't specify groups between which to find hydrogen bonds 2189s hbonds = HydrogenBondAnalysis(universe, between=None, **self.kwargs) 2189s > hbonds.run(**client_HydrogenBondAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:451: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisBetween.test_between_PW[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_between_PW(self, universe, client_HydrogenBondAnalysis): 2189s # Find only protein-water hydrogen bonds 2189s hbonds = HydrogenBondAnalysis( 2189s universe, 2189s between=["resname PROT", "resname SOL"], 2189s **self.kwargs 2189s ) 2189s > hbonds.run(**client_HydrogenBondAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:471: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisBetween.test_between_PW_PP[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_between_PW_PP(self, universe, client_HydrogenBondAnalysis): 2189s # Find protein-water and protein-protein hydrogen bonds (not 2189s # water-water) 2189s hbonds = HydrogenBondAnalysis( 2189s universe, 2189s between=[ 2189s ["resname PROT", "resname SOL"], 2189s ["resname PROT", "resname PROT"] 2189s ], 2189s **self.kwargs 2189s ) 2189s > hbonds.run(**client_HydrogenBondAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:493: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_.test_no_hydrogens[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_no_hydrogens(self, universe, client_HydrogenBondAnalysis): 2189s # If no hydrogens are identified at a given frame, check an 2189s # empty donor atom group is created 2189s test_kwargs = TestHydrogenBondAnalysisTIP3P.kwargs.copy() 2189s test_kwargs['donors_sel'] = None # use topology to find pairs 2189s test_kwargs['hydrogens_sel'] = "name H" # no atoms have name H 2189s 2189s h = HydrogenBondAnalysis(universe, **test_kwargs) 2189s > h.run(**client_HydrogenBondAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:527: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _ TestHydrogenBondAnalysisEmptySelections.test_hbond_analysis[client_HydrogenBondAnalysis0] _ 2189s 2189s self = 2189s universe = 2189s client_HydrogenBondAnalysis = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_hbond_analysis(self, universe, client_HydrogenBondAnalysis): 2189s 2189s h = HydrogenBondAnalysis(universe, donors_sel=' ', hydrogens_sel=' ', 2189s acceptors_sel=' ') 2189s > h.run(**client_HydrogenBondAnalysis) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py:701: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _______________________ TestRMSD.test_rmsd[client_RMSD0] _______________________ 2189s 2189s self = 2189s universe = 2189s correct_values = [[0, 1, 0], [49, 50, 4.68953]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd(self, universe, correct_values, client_RMSD): 2189s # client_RMSD is defined in testsuite/analysis/conftest.py 2189s # among with other testing fixtures. During testing, it will 2189s # collect all possible backends and reasonable number of workers 2189s # for a given AnalysisBase subclass, and extend the tests 2189s # to run with all of them. 2189s RMSD = MDAnalysis.analysis.rms.RMSD(universe, select='name CA') 2189s > RMSD.run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:196: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ___________________ TestRMSD.test_rmsd_frames[client_RMSD0] ____________________ 2189s 2189s self = 2189s universe = 2189s correct_values = [[0, 1, 0], [49, 50, 4.68953]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_frames(self, universe, correct_values, client_RMSD): 2189s RMSD = MDAnalysis.analysis.rms.RMSD(universe, select='name CA') 2189s > RMSD.run(frames=[0, 49], **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:203: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ______________ TestRMSD.test_rmsd_unicode_selection[client_RMSD0] ______________ 2189s 2189s self = 2189s universe = 2189s correct_values = [[0, 1, 0], [49, 50, 4.68953]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_unicode_selection(self, universe, correct_values, client_RMSD): 2189s RMSD = MDAnalysis.analysis.rms.RMSD(universe, select=u'name CA') 2189s > RMSD.run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:210: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ____________ TestRMSD.test_rmsd_atomgroup_selections[client_RMSD0] _____________ 2189s 2189s self = 2189s universe = 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_atomgroup_selections(self, universe, client_RMSD): 2189s # see Issue #1684 2189s > R1 = MDAnalysis.analysis.rms.RMSD(universe.atoms, 2189s select="resid 1-30").run(**client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:217: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________________ TestRMSD.test_rmsd_single_frame[client_RMSD0] _________________ 2189s 2189s self = 2189s universe = 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_single_frame(self, universe, client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, select='name CA', 2189s ).run(start=5, stop=6, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:224: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________ TestRMSD.test_mass_weighted[client_RMSD0] ___________________ 2189s 2189s self = 2189s universe = 2189s correct_values = [[0, 1, 0], [49, 50, 4.68953]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_mass_weighted(self, universe, correct_values, client_RMSD): 2189s # mass weighting the CA should give the same answer as weighing 2189s # equally because all CA have the same mass 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, select='name CA', 2189s weights='mass').run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:234: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _________________ TestRMSD.test_custom_weighted[client_RMSD0] __________________ 2189s 2189s self = 2189s universe = 2189s correct_values_mass = [[0, 1, 0], [49, 50, 4.7492]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_custom_weighted(self, universe, correct_values_mass, client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, weights="mass").run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:242: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________ TestRMSD.test_weights_mass_is_mass_weighted[client_RMSD0] ___________ 2189s 2189s self = 2189s universe = 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_weights_mass_is_mass_weighted(self, universe, client_RMSD): 2189s > RMSD_mass = MDAnalysis.analysis.rms.RMSD(universe, 2189s weights="mass").run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:249: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s _______________ TestRMSD.test_custom_weighted_list[client_RMSD0] _______________ 2189s 2189s self = 2189s universe = 2189s correct_values_mass = [[0, 1, 0], [49, 50, 4.7492]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_custom_weighted_list(self, universe, correct_values_mass, client_RMSD): 2189s weights = universe.atoms.masses 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, 2189s weights=list(weights)).run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:259: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __ TestRMSD.test_custom_groupselection_weights_applied_1D_array[client_RMSD0] __ 2189s 2189s self = 2189s universe = 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_custom_groupselection_weights_applied_1D_array(self, universe, client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, 2189s select='backbone', 2189s groupselections=['name CA and resid 1-5', 'name CA and resid 1'], 2189s weights=None, 2189s weights_groupselections=[[1, 0, 0, 0, 0], None]).run(step=49, 2189s **client_RMSD 2189s ) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:266: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ____ TestRMSD.test_custom_groupselection_weights_applied_mass[client_RMSD0] ____ 2189s 2189s self = 2189s universe = 2189s correct_values_mass = [[0, 1, 0], [49, 50, 4.7492]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_custom_groupselection_weights_applied_mass(self, universe, correct_values_mass, client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, 2189s select='backbone', 2189s groupselections=['all', 'all'], 2189s weights=None, 2189s weights_groupselections=['mass', 2189s universe.atoms.masses]).run(step=49, 2189s **client_RMSD 2189s ) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:279: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ______________ TestRMSD.test_rmsd_group_selections[client_RMSD0] _______________ 2189s 2189s self = 2189s universe = 2189s correct_values_group = [[0, 1, 0, 0, 0], [49, 50, 4.7857, 4.7048, 4.6924]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_group_selections(self, universe, correct_values_group, client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD(universe, 2189s groupselections=['backbone', 'name CA'] 2189s ).run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:328: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________ TestRMSD.test_rmsd_backbone_and_group_selection[client_RMSD0] _________ 2189s 2189s self = 2189s universe = 2189s correct_values_backbone_group = [[0, 1, 0, 0, 0], [49, 50, 4.6997, 1.9154, 2.7139]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_backbone_and_group_selection(self, universe, 2189s correct_values_backbone_group, 2189s client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD( 2189s universe, 2189s reference=universe, 2189s select="backbone", 2189s groupselections=['backbone and resid 1:10', 2189s 'backbone and resid 10:20']).run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:338: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ____________ TestRMSD.test_ref_mobile_mass_mismapped[client_RMSD0] _____________ 2189s 2189s self = 2189s universe = 2189s correct_values_mass_add_ten = [[0, 1, 0.0632], [49, 50, 4.771]] 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_ref_mobile_mass_mismapped(self, universe,correct_values_mass_add_ten, client_RMSD): 2189s reference = MDAnalysis.Universe(PSF, DCD) 2189s universe.atoms.masses = universe.atoms.masses + 10 2189s RMSD = MDAnalysis.analysis.rms.RMSD(universe, 2189s reference=reference, 2189s select='all', 2189s weights='mass', 2189s tol_mass=100) 2189s > RMSD.run(step=49, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:370: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________________ TestRMSD.test_rmsd_attr_warning[client_RMSD0] _________________ 2189s 2189s self = 2189s universe = 2189s client_RMSD = {'backend': 'multiprocessing', 'n_workers': 2} 2189s 2189s def test_rmsd_attr_warning(self, universe, client_RMSD): 2189s > RMSD = MDAnalysis.analysis.rms.RMSD( 2189s universe, select='name CA').run(stop=2, **client_RMSD) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/analysis/test_rms.py:384: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:822: in run 2189s remote_objects: list["AnalysisBase"] = executor.apply( 2189s /usr/lib/python3/dist-packages/MDAnalysis/analysis/backends.py:252: in apply 2189s with Pool(processes=self.n_workers) as pool: 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u0] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u1] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u2] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u3] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u4] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u5] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u6] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u7] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u8] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u9] ___________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u10] __________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u11] __________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u12] __________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u13] __________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s __________________________ test_multiprocess_COG[u14] __________________________ 2189s 2189s u = 2189s 2189s def test_multiprocess_COG(u): 2189s ag = u.atoms[2:5] 2189s 2189s ref = np.array([cog(u, ag, i) 2189s for i in range(3)]) 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:126: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ____________________ test_universe_unpickle_in_new_process _____________________ 2189s 2189s def test_universe_unpickle_in_new_process(): 2189s u = mda.Universe(GRO, XTC) 2189s ref = [getnames(u, i) 2189s for i in range(3)] 2189s 2189s > p = multiprocessing.Pool(2) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:143: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ________________ test_creating_multiple_universe_without_offset ________________ 2189s 2189s temp_xtc = PosixPath('/tmp/pytest-of-ubuntu/pytest-1/test_creating_multiple_univers0/testing.xtc') 2189s ncopies = 3 2189s 2189s def test_creating_multiple_universe_without_offset(temp_xtc, ncopies=3): 2189s # test if they can be created without generating 2189s # the offset simultaneously. 2189s # The tested XTC file is way too short to induce a race scenario but the 2189s # test is included as documentation for the scenario that used to create 2189s # a problem (see PR #3375 and issues #3230, #1988) 2189s 2189s args = (GRO, str(temp_xtc)) 2189s > with multiprocessing.Pool(2) as p: 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:159: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ______________________________ test_streamplot_2D ______________________________ 2189s 2189s membrane_xtc = '/tmp/pytest-of-ubuntu/pytest-1/streamlines0/dummy.xtc' 2189s univ = 2189s 2189s def test_streamplot_2D(membrane_xtc, univ): 2189s # regression test the data structures 2189s # generated by the 2D streamplot code 2189s > u1, v1, avg, std = streamlines.generate_streamlines(topology_file_path=Martini_membrane_gro, 2189s trajectory_file_path=membrane_xtc, 2189s grid_spacing=20, 2189s MDA_selection='name PO4', 2189s start_frame=1, 2189s end_frame=2, 2189s xmin=univ.atoms.positions[...,0].min(), 2189s xmax=univ.atoms.positions[...,0].max(), 2189s ymin=univ.atoms.positions[...,1].min(), 2189s ymax=univ.atoms.positions[...,1].max(), 2189s maximum_delta_magnitude=2.0, 2189s num_cores=1) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/visualization/test_streamlines.py:57: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/visualization/streamlines.py:330: in generate_streamlines 2189s pool = multiprocessing.Pool(num_cores) 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ------------------------------ Captured log setup ------------------------------ 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:653 Universe.load_new(): loading /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/martini_dppc_chol_bilayer.gro... 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s INFO MDAnalysis.core.universe:universe.py:1682 attribute types has been guessed successfully. 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s INFO MDAnalysis.core.universe:universe.py:1682 attribute masses has been guessed successfully. 2189s ________________________ test_streamplot_2D_zero_return ________________________ 2189s 2189s membrane_xtc = '/tmp/pytest-of-ubuntu/pytest-1/streamlines0/dummy.xtc' 2189s univ = 2189s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_streamplot_2D_zero_return0') 2189s 2189s def test_streamplot_2D_zero_return(membrane_xtc, univ, tmpdir): 2189s # simple roundtrip test to ensure that 2189s # zeroed arrays are returned by the 2D streamplot 2189s # code when called with an empty selection 2189s > u1, v1, avg, std = streamlines.generate_streamlines(topology_file_path=Martini_membrane_gro, 2189s trajectory_file_path=membrane_xtc, 2189s grid_spacing=20, 2189s MDA_selection='name POX', 2189s start_frame=1, 2189s end_frame=2, 2189s xmin=univ.atoms.positions[...,0].min(), 2189s xmax=univ.atoms.positions[...,0].max(), 2189s ymin=univ.atoms.positions[...,1].min(), 2189s ymax=univ.atoms.positions[...,1].max(), 2189s maximum_delta_magnitude=2.0, 2189s num_cores=1) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/visualization/test_streamlines.py:87: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/visualization/streamlines.py:330: in generate_streamlines 2189s pool = multiprocessing.Pool(num_cores) 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ______________________________ test_streamplot_3D ______________________________ 2189s 2189s membrane_xtc = '/tmp/pytest-of-ubuntu/pytest-1/streamlines0/dummy.xtc' 2189s univ = 2189s tmpdir = local('/tmp/pytest-of-ubuntu/pytest-1/test_streamplot_3D0') 2189s 2189s def test_streamplot_3D(membrane_xtc, univ, tmpdir): 2189s # because mayavi is too heavy of a dependency 2189s # for a roundtrip plotting test, simply 2189s # aim to check for sensible values 2189s # returned by generate_streamlines_3d 2189s > dx, dy, dz = streamlines_3D.generate_streamlines_3d(topology_file_path=Martini_membrane_gro, 2189s trajectory_file_path=membrane_xtc, 2189s grid_spacing=20, 2189s MDA_selection='name PO4', 2189s start_frame=1, 2189s end_frame=2, 2189s xmin=univ.atoms.positions[...,0].min(), 2189s xmax=univ.atoms.positions[...,0].max(), 2189s ymin=univ.atoms.positions[...,1].min(), 2189s ymax=univ.atoms.positions[...,1].max(), 2189s zmin=univ.atoms.positions[...,2].min(), 2189s zmax=univ.atoms.positions[...,2].max(), 2189s maximum_delta_magnitude=2.0, 2189s num_cores=1) 2189s 2189s /tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/visualization/test_streamlines.py:110: 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s /usr/lib/python3/dist-packages/MDAnalysis/visualization/streamlines_3D.py:468: in generate_streamlines_3d 2189s pool = multiprocessing.Pool(num_cores) 2189s /usr/lib/python3.13/multiprocessing/context.py:119: in Pool 2189s return Pool(processes, initializer, initargs, maxtasksperchild, 2189s /usr/lib/python3.13/multiprocessing/pool.py:215: in __init__ 2189s self._repopulate_pool() 2189s /usr/lib/python3.13/multiprocessing/pool.py:306: in _repopulate_pool 2189s return self._repopulate_pool_static(self._ctx, self.Process, 2189s /usr/lib/python3.13/multiprocessing/pool.py:329: in _repopulate_pool_static 2189s w.start() 2189s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2189s 2189s self = 2189s 2189s def start(self): 2189s ''' 2189s Start child process 2189s ''' 2189s self._check_closed() 2189s assert self._popen is None, 'cannot start a process twice' 2189s assert self._parent_pid == os.getpid(), \ 2189s 'can only start a process object created by current process' 2189s > assert not _current_process._config.get('daemon'), \ 2189s 'daemonic processes are not allowed to have children' 2189s E AssertionError: daemonic processes are not allowed to have children 2189s 2189s /usr/lib/python3.13/multiprocessing/process.py:118: AssertionError 2189s ------------------------------ Captured log call ------------------------------- 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s DEBUG MDAnalysis.core.universe:universe.py:653 Universe.load_new(): loading /tmp/pytest-of-ubuntu/pytest-1/streamlines0/dummy.xtc... 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s INFO MDAnalysis.core.universe:universe.py:1682 attribute types has been guessed successfully. 2189s DEBUG MDAnalysis.core.universe:universe.py:1014 _process_attr: Adding to topology 2189s INFO MDAnalysis.core.universe:universe.py:1682 attribute masses has been guessed successfully. 2189s =========================== short test summary info ============================ 2189s FAILED testsuite/MDAnalysisTests/analysis/test_base.py::test_AnalysisFromFunction[client_AnalysisFromFunction0-None-None-2-49] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_base.py::test_AnalysisFromFunction[client_AnalysisFromFunction0-None-50-2-25] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_base.py::test_AnalysisFromFunction[client_AnalysisFromFunction0-20-50-2-15] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_base.py::test_AnalysisFromFunction[client_AnalysisFromFunction0-20-50-None-30] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_base.py::test_AnalysisFromFunction_args_content[client_AnalysisFromFunction0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_coordinates_single_frame[client_BAT0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral[client_Dihedral0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_single_frame[client_Dihedral0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_atomgroup_list[client_Dihedral0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_attr_warning[client_Dihedral0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran[client_Ramachandran0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame[client_Ramachandran0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections[client_Ramachandran0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_outside_protein_unchecked[client_Ramachandran0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin[client_Janin0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr[client_Janin0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_residue_selections[client_Janin0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1ahsA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1bvyF.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1dx5I.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1eteA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1h4aX.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1i8nA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1lpbA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1mr1D.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1or4A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1pdoA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1v7mV.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/1y1lA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2a2lA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2cayA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2cviA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2fvvA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2gu3A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2i39A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2j49A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2qdlA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2va0A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xcjA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xdgA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/2xr6A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3a4rA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3aqgA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3e8mA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ejfA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3fhkA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gfsA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gknA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3gwiA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3hklA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ieyB.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ii2A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3k7pA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3l4rA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3lqcA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nbkA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nngA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3ny7A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3nzmA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3on9A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3pivA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3q4oA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3so6A.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3t5gB.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/3vjzA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/4dkcA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_file_guess_hydrogens[client_DSSP0-/tmp/autopkgtest.MV1swv/build.5yX/src/testsuite/MDAnalysisTests/data/dssp/4gcnA.pdb.gz] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory[client_DSSP0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_atomgroup[client_DSSP0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_dssp.py::test_trajectory_with_hydrogens[client_DSSP0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_encore.py::TestEncore::test_parallel_calculation 2189s FAILED testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm[client_GNMAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_gnm.py::test_gnm_run_step[client_GNMAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_gnm.py::test_closeContactGNMAnalysis[client_GNMAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_gnm.py::test_closeContactGNMAnalysis_weights_None[client_GNMAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisBetween::test_between_all[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisBetween::test_between_PW[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisBetween::test_between_PW_PP[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis[client_HydrogenBondAnalysis0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_frames[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_unicode_selection[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_atomgroup_selections[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_single_frame[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_mass_weighted[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_custom_weighted[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_weights_mass_is_mass_weighted[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_custom_weighted_list[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_custom_groupselection_weights_applied_1D_array[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_custom_groupselection_weights_applied_mass[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_group_selections[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_backbone_and_group_selection[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_ref_mobile_mass_mismapped[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/analysis/test_rms.py::TestRMSD::test_rmsd_attr_warning[client_RMSD0] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u0] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u1] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u8] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u9] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u12] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u13] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_universe_unpickle_in_new_process 2189s FAILED testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_creating_multiple_universe_without_offset 2189s FAILED testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 2189s FAILED testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D_zero_return 2189s FAILED testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_3D 2189s ERROR testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_number_of_frames[client_BAT0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_coordinates[client_BAT0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_reconstruction[client_BAT0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_IO[client_BAT0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_bat_incorrect_dims[client_BAT0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_bat.py::TestBAT::test_Cartesian_does_not_modify_input[client_BAT0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_hbond_analysis[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_count_by_time[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_count_by_type[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_count_by_ids[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P::test_hbonds_deprecated_attr[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_first_hbond[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_time[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_hydrogen_bond_lifetime[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_hydrogen_bond_lifetime_intermittency[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_first_hbond[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_time[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_hydrogen_bond_lifetime[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_hydrogen_bond_lifetime_intermittency[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_hbond_analysis[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_count_by_time[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_count_by_type[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_count_by_ids[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_hbonds_deprecated_attr[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3PStartStep::test_hbond_analysis[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3PStartStep::test_count_by_time[client_HydrogenBondAnalysis0] 2189s ERROR testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3PStartStep::test_count_by_type[client_HydrogenBondAnalysis0] 2189s = 117 failed, 18958 passed, 558 skipped, 2 deselected, 7 xfailed, 2 xpassed, 104301 warnings, 29 errors in 805.07s (0:13:25) = 2220s ............ [ 0%] 2223s testsuite/MDAnalysisTests/analysis/test_bat.py ................... [ 0%] 2224s testsuite/MDAnalysisTests/analysis/test_contacts.py .................... [ 1%] 2244s ................ [ 1%] 2244s testsuite/MDAnalysisTests/analysis/test_data.py . [ 1%] 2244s testsuite/MDAnalysisTests/analysis/test_density.py ..................... [ 1%] 2251s ...................... [ 1%] 2251s testsuite/MDAnalysisTests/analysis/test_dielectric.py ...... [ 1%] 2256s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py ........... [ 1%] 2264s testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [ 1%] 2271s ....................... [ 1%] 2277s testsuite/MDAnalysisTests/analysis/test_distances.py ............ [ 1%] 2281s testsuite/MDAnalysisTests/analysis/test_dssp.py ........................ [ 1%] 2292s ........................................................................ [ 2%] 2294s ................ [ 2%] 2325s testsuite/MDAnalysisTests/analysis/test_encore.py ..................X..X [ 2%] 2344s ...................................... [ 2%] 2364s testsuite/MDAnalysisTests/analysis/test_gnm.py .......... [ 2%] 2364s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py .............. [ 2%] 2365s ................................ [ 2%] 2365s testsuite/MDAnalysisTests/analysis/test_hole2.py s [ 2%] 2366s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [ 2%] 2366s ......... [ 2%] 2366s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [ 2%] 2367s ................. [ 3%] 2368s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py ...... [ 3%] 2369s .................................................................... [ 3%] 2371s testsuite/MDAnalysisTests/analysis/test_leaflet.py s............ [ 3%] 2371s testsuite/MDAnalysisTests/analysis/test_lineardensity.py ........ [ 3%] 2373s testsuite/MDAnalysisTests/analysis/test_msd.py .......................ss [ 3%] 2373s sssssssssssssssssssssssssssss [ 3%] 2375s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [ 3%] 2375s [ 3%] 2375s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py .................... [ 3%] 2375s .............. [ 4%] 2378s testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [ 4%] 2379s ......................... [ 4%] 2382s testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [ 4%] 2382s ....... [ 4%] 2382s testsuite/MDAnalysisTests/analysis/test_psa.py s [ 4%] 2383s testsuite/MDAnalysisTests/analysis/test_rdf.py .................... [ 4%] 2384s testsuite/MDAnalysisTests/analysis/test_rdf_s.py ..................... [ 4%] 2384s testsuite/MDAnalysisTests/analysis/test_results.py ..................... [ 4%] 2384s ........................................................................ [ 5%] 2384s ............................................... [ 5%] 2398s testsuite/MDAnalysisTests/analysis/test_rms.py ......................... [ 5%] 2407s ................................... [ 5%] 2407s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py s [ 5%] 2407s testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [ 5%] 2407s ........................... [ 5%] 2407s testsuite/MDAnalysisTests/auxiliary/test_core.py ..... [ 5%] 2407s testsuite/MDAnalysisTests/auxiliary/test_edr.py .sssssssssssssssssssssss [ 6%] 2407s ssssssssssssssssssssssssssssssssssssssssssss [ 6%] 2407s testsuite/MDAnalysisTests/auxiliary/test_xvg.py ........................ [ 6%] 2407s ........................................................................ [ 6%] 2407s .... [ 6%] 2407s testsuite/MDAnalysisTests/converters/test_base.py .. [ 6%] 2407s testsuite/MDAnalysisTests/converters/test_rdkit.py .ssssssssssssssssssss [ 6%] 2407s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 7%] 2408s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 7%] 2408s ssssssssssssssssssssssssssssss [ 7%] 2408s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ... [ 7%] 2411s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [ 7%] 2421s ........................................................ [ 8%] 2422s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [ 8%] 2430s ...............................................................ss.ss.s.s [ 8%] 2439s s.sss....ss...s.ssss.ss.s.ss.sss....ss...s.ssss.ss.s.ss.sss....ss.s.ssss [ 8%] 2445s .......................................................s [ 9%] 2446s testsuite/MDAnalysisTests/coordinates/test_crd.py .............. [ 9%] 2446s testsuite/MDAnalysisTests/coordinates/test_dcd.py ...................... [ 9%] 2448s .......x.......ss....................................................... [ 9%] 2450s ..........................................s [ 10%] 2450s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [ 10%] 2450s .................................... [ 10%] 2452s testsuite/MDAnalysisTests/coordinates/test_dms.py ......... [ 10%] 2452s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [ 10%] 2452s ....... [ 10%] 2452s testsuite/MDAnalysisTests/coordinates/test_gms.py .................. [ 10%] 2453s testsuite/MDAnalysisTests/coordinates/test_gro.py ...................... [ 10%] 2455s .......................sss.............................................. [ 11%] 2455s ..............sss...................................................sss. [ 11%] 2474s ..................................................sss................... [ 11%] 2485s .................... [ 11%] 2485s testsuite/MDAnalysisTests/coordinates/test_gsd.py ss.... [ 11%] 2486s testsuite/MDAnalysisTests/coordinates/test_h5md.py ..................... [ 12%] 2491s ..............ss........................................................ [ 12%] 2507s .......x..................................................... [ 12%] 2508s testsuite/MDAnalysisTests/coordinates/test_lammps.py ................... [ 12%] 2517s ........................................................................ [ 13%] 2549s ................................................................. [ 13%] 2551s testsuite/MDAnalysisTests/coordinates/test_memory.py ................... [ 13%] 2562s ........x......xxx...................................................... [ 13%] 2562s .......................... [ 14%] 2562s testsuite/MDAnalysisTests/coordinates/test_mmtf.py ............ [ 14%] 2563s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 14%] 2563s [ 14%] 2563s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 14%] 2564s ..... [ 14%] 2564s testsuite/MDAnalysisTests/coordinates/test_netcdf.py ................... [ 14%] 2566s ........................................................................ [ 14%] 2570s ........................................................................ [ 15%] 2571s .................. [ 15%] 2571s testsuite/MDAnalysisTests/coordinates/test_null.py . [ 15%] 2572s testsuite/MDAnalysisTests/coordinates/test_pdb.py ...................... [ 15%] 2594s ........................................................................ [ 15%] 2598s ........................................................................ [ 16%] 2599s ................ [ 16%] 2599s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py ............... [ 16%] 2601s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 16%] 2601s ........ [ 16%] 2601s testsuite/MDAnalysisTests/coordinates/test_reader_api.py ............... [ 16%] 2601s ........................................................................ [ 16%] 2601s ........................................................................ [ 17%] 2601s ............................. [ 17%] 2601s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py ............. [ 17%] 2601s ........................................................................ [ 17%] 2605s ........................................................................ [ 18%] 2606s ................. [ 18%] 2606s testsuite/MDAnalysisTests/coordinates/test_tng.py ..ssssssssssssssssssss [ 18%] 2606s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 18%] 2606s s [ 18%] 2607s testsuite/MDAnalysisTests/coordinates/test_trc.py ...................... [ 18%] 2607s .......... [ 18%] 2607s testsuite/MDAnalysisTests/coordinates/test_trj.py ...................... [ 19%] 2608s .............. [ 19%] 2609s testsuite/MDAnalysisTests/coordinates/test_trz.py ...................... [ 19%] 2609s .. [ 19%] 2609s testsuite/MDAnalysisTests/coordinates/test_txyz.py ...... [ 19%] 2609s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 19%] 2610s ........................................................... [ 19%] 2610s testsuite/MDAnalysisTests/coordinates/test_writer_api.py .ss............ [ 19%] 2611s ......ss.....s............ss.....s........... [ 19%] 2611s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py .... [ 19%] 2612s testsuite/MDAnalysisTests/coordinates/test_xdr.py ...................... [ 20%] 2624s ........................................................................ [ 20%] 2624s ....ss.................................................................. [ 20%] 2625s .ss......................................................... [ 21%] 2625s testsuite/MDAnalysisTests/coordinates/test_xyz.py ...................... [ 21%] 2626s ...............ss....................................................... [ 21%] 2626s .................ss....................................... [ 21%] 2626s testsuite/MDAnalysisTests/core/test_accessors.py ssss..s [ 21%] 2628s testsuite/MDAnalysisTests/core/test_accumulate.py ...................... [ 22%] 2635s ................................................................... [ 22%] 2637s testsuite/MDAnalysisTests/core/test_atom.py .................... [ 22%] 2641s testsuite/MDAnalysisTests/core/test_atomgroup.py ....................... [ 22%] 2653s ........................................................................ [ 22%] 2654s ........................................................................ [ 23%] 2666s ........................................................................ [ 23%] 2685s ........................................................................ [ 24%] 2700s ........................................................................ [ 24%] 2706s .......................................................... [ 24%] 2706s testsuite/MDAnalysisTests/core/test_atomselections.py .................. [ 24%] 2706s ........................................................................ [ 25%] 2708s ........................................................................ [ 25%] 2722s ..................sssssssssssssssssss................................... [ 25%] 2723s ........................................................................ [ 26%] 2723s ........................................................................ [ 26%] 2724s ........................................................................ [ 27%] 2736s .....................................sssss...........ssssss.... [ 27%] 2736s testsuite/MDAnalysisTests/core/test_copying.py ......................... [ 27%] 2736s .................... [ 27%] 2738s testsuite/MDAnalysisTests/core/test_fragments.py ................ [ 27%] 2738s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%] 2741s ................................................. [ 27%] 2741s testsuite/MDAnalysisTests/core/test_groups.py .......................... [ 28%] 2741s ........................................................................ [ 28%] 2741s ........................................................................ [ 28%] 2741s ........................................................................ [ 29%] 2743s ........................................................................ [ 29%] 2743s ........................................................................ [ 29%] 2743s ........................................................................ [ 30%] 2743s ........................................................................ [ 30%] 2763s ....................................................................... [ 31%] 2763s testsuite/MDAnalysisTests/core/test_index_dtype.py ............... [ 31%] 2763s testsuite/MDAnalysisTests/core/test_requires.py .... [ 31%] 2764s testsuite/MDAnalysisTests/core/test_residue.py .... [ 31%] 2765s testsuite/MDAnalysisTests/core/test_residuegroup.py s..................s [ 31%] 2766s ssss..... [ 31%] 2767s testsuite/MDAnalysisTests/core/test_segment.py ....... [ 31%] 2767s testsuite/MDAnalysisTests/core/test_segmentgroup.py ........... [ 31%] 2767s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%] 2768s ........................................ [ 31%] 2769s testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%] 2769s ...................................................................x.... [ 32%] 2770s ........................................................ [ 32%] 2770s testsuite/MDAnalysisTests/core/test_topologyobjects.py ................. [ 32%] 2773s ...................................................................... [ 32%] 2775s testsuite/MDAnalysisTests/core/test_universe.py .................sssssss [ 33%] 2780s s....................................................................... [ 33%] 2783s ........................................................................ [ 33%] 2786s ........................................................................ [ 34%] 2788s .................................... [ 34%] 2788s testsuite/MDAnalysisTests/core/test_unwrap.py .......................... [ 34%] 2789s ........................................................................ [ 34%] 2789s ........................................................................ [ 35%] 2790s ........................................................................ [ 35%] 2790s ........................................................................ [ 35%] 2790s ........................................................................ [ 36%] 2790s ........................................................................ [ 36%] 2791s ................................................... [ 36%] 2793s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py .............. [ 36%] 2793s . [ 36%] 2794s testsuite/MDAnalysisTests/core/test_wrap.py ............................ [ 37%] 2794s ........................................................................ [ 37%] 2795s ........................................................................ [ 37%] 2795s ........................................................................ [ 38%] 2795s ........................................................................ [ 38%] 2796s ........................................................................ [ 38%] 2796s ........................................................................ [ 39%] 2797s ......................................................... [ 39%] 2797s testsuite/MDAnalysisTests/formats/test_libdcd.py ....................... [ 39%] 2799s ........................................................................ [ 40%] 2799s ...... [ 40%] 2799s testsuite/MDAnalysisTests/formats/test_libmdaxdr.py .................... [ 40%] 2799s ........................................................................ [ 40%] 2799s ... [ 40%] 2836s testsuite/MDAnalysisTests/guesser/test_base.py ........................ [ 40%] 2836s testsuite/MDAnalysisTests/guesser/test_default_guesser.py .............. [ 40%] 2837s ...........................sssssssssss [ 40%] 2837s testsuite/MDAnalysisTests/import/test_import.py .. [ 40%] 2837s testsuite/MDAnalysisTests/lib/test_augment.py .......................... [ 41%] 2837s .......... [ 41%] 2837s testsuite/MDAnalysisTests/lib/test_cutil.py ............. [ 41%] 2838s testsuite/MDAnalysisTests/lib/test_distances.py ........................ [ 41%] 2838s ........................................................................ [ 41%] 2838s ........................................................................ [ 42%] 2838s ........................................................................ [ 42%] 2838s ........................................................................ [ 42%] 2839s ........................................................................ [ 43%] 2839s ........................................................................ [ 43%] 2846s ........................................................................ [ 43%] 2849s ........................................................................ [ 44%] 2849s ........................................................................ [ 44%] 2849s ........................................................................ [ 45%] 2850s ........................................................................ [ 45%] 2850s ........................................................................ [ 45%] 2850s ........................................................................ [ 46%] 2850s ........................................................................ [ 46%] 2851s ........................................................................ [ 46%] 2851s ........................................................................ [ 47%] 2851s ........................................................................ [ 47%] 2851s ........................................................................ [ 47%] 2851s ........................................................................ [ 48%] 2851s ........................................................................ [ 48%] 2851s ........................................................................ [ 49%] 2851s ........................................................................ [ 49%] 2852s ........................................................................ [ 49%] 2852s ........................................................................ [ 50%] 2852s ........................................................................ [ 50%] 2852s ........................................................................ [ 50%] 2852s ........................................................................ [ 51%] 2852s ........................................................................ [ 51%] 2852s ........................................................................ [ 51%] 2852s ........................................................................ [ 52%] 2853s ........................................................................ [ 52%] 2853s ........................................................................ [ 53%] 2853s ........................................................................ [ 53%] 2853s ........................................................................ [ 53%] 2853s ............................................... [ 54%] 2853s testsuite/MDAnalysisTests/lib/test_log.py ... [ 54%] 2853s testsuite/MDAnalysisTests/lib/test_neighborsearch.py .. [ 54%] 2858s testsuite/MDAnalysisTests/lib/test_nsgrid.py ........................... [ 54%] 2858s ..s [ 54%] 2858s testsuite/MDAnalysisTests/lib/test_pkdtree.py ................. [ 54%] 2858s testsuite/MDAnalysisTests/lib/test_qcprot.py .... [ 54%] 2859s testsuite/MDAnalysisTests/lib/test_util.py ............................. [ 54%] 2859s ........................................................................ [ 54%] 2859s ........................................................................ [ 55%] 2859s ........................................................................ [ 55%] 2859s ........................................................................ [ 55%] 2859s ........................................................................ [ 56%] 2859s ........................................................................ [ 56%] 2859s ........................................................................ [ 57%] 2859s ........................................................................ [ 57%] 2859s ........................................................................ [ 57%] 2859s ........................................................................ [ 58%] 2859s ........................................................................ [ 58%] 2860s ........................................................................ [ 58%] 2860s ........................................................................ [ 59%] 2860s ........................................................................ [ 59%] 2860s ........................................................................ [ 59%] 2860s ........................................................................ [ 60%] 2860s ........................................................................ [ 60%] 2860s ........................................................................ [ 61%] 2860s ........................................................................ [ 61%] 2860s ........................................................................ [ 61%] 2860s ........................................................................ [ 62%] 2860s ........................................................................ [ 62%] 2861s ........................................................................ [ 62%] 2861s ........................................................................ [ 63%] 2861s ........................................................................ [ 63%] 2861s ........................................................................ [ 63%] 2861s ........................................................................ [ 64%] 2861s ........................................................................ [ 64%] 2861s ........................................................................ [ 65%] 2861s ........................................................................ [ 65%] 2861s ........................................................................ [ 65%] 2862s ........................................................................ [ 66%] 2862s ........................................................................ [ 66%] 2862s ........................................................................ [ 66%] 2862s ........................................................................ [ 67%] 2862s ........................................................................ [ 67%] 2862s ........................................................................ [ 68%] 2862s ........................................................................ [ 68%] 2862s ........................................................................ [ 68%] 2862s ........................................................................ [ 69%] 2862s ........................................................................ [ 69%] 2863s ........................................................................ [ 69%] 2863s ........................................................................ [ 70%] 2863s ........................................................................ [ 70%] 2863s ........................................................................ [ 70%] 2863s ........................................................................ [ 71%] 2863s ........................................................................ [ 71%] 2863s ........................................................................ [ 72%] 2863s ........................................................................ [ 72%] 2863s ........................................................................ [ 72%] 2863s ........................................................................ [ 73%] 2864s ........................................................................ [ 73%] 2864s ........................................................................ [ 73%] 2864s ........................................................................ [ 74%] 2864s ........................................................................ [ 74%] 2864s ........................................................................ [ 74%] 2864s ........................................................................ [ 75%] 2864s ........................................................................ [ 75%] 2864s ........................................................................ [ 76%] 2864s ........................................................................ [ 76%] 2864s ........................................................................ [ 76%] 2864s ........................................................................ [ 77%] 2865s ........................................................................ [ 77%] 2865s ........................................................................ [ 77%] 2865s ........................................................................ [ 78%] 2865s ........................................................................ [ 78%] 2865s ........................................................................ [ 79%] 2865s ........................................................................ [ 79%] 2865s ........................................................................ [ 79%] 2865s ........................................................................ [ 80%] 2865s ........................................................................ [ 80%] 2867s ........................................................................ [ 80%] 2867s ........................................................................ [ 81%] 2867s ........................................................................ [ 81%] 2867s ........................................................................ [ 81%] 2867s ........................................................................ [ 82%] 2867s ........................................................................ [ 82%] 2867s ........................................................................ [ 83%] 2867s ........................................................................ [ 83%] 2868s .........................................s.............................. [ 83%] 2868s ........................................................................ [ 84%] 2868s .............s.......................................................... [ 84%] 2875s ........................................................................ [ 84%] 2875s ..................................................... [ 85%] 2878s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py .......... [ 85%] 2897s ....................................... [ 85%] 2897s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py .... [ 85%] 2897s .... [ 85%] 2897s testsuite/MDAnalysisTests/test_api.py ................................. [ 85%] 2902s testsuite/MDAnalysisTests/topology/test_altloc.py ... [ 85%] 2903s testsuite/MDAnalysisTests/topology/test_crd.py .......... [ 85%] 2903s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 85%] 2903s .............................................. [ 86%] 2904s testsuite/MDAnalysisTests/topology/test_dms.py ...................... [ 86%] 2904s testsuite/MDAnalysisTests/topology/test_fhiaims.py ............ [ 86%] 2904s testsuite/MDAnalysisTests/topology/test_gms.py ......................... [ 86%] 2905s ......... [ 86%] 2907s testsuite/MDAnalysisTests/topology/test_gro.py ................. [ 86%] 2907s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%] 2907s ...... [ 86%] 2907s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 86%] 2908s ..............ssssssssss..........s [ 86%] 2908s testsuite/MDAnalysisTests/topology/test_hoomdxml.py .................. [ 86%] 2908s testsuite/MDAnalysisTests/topology/test_itp.py ......................... [ 87%] 2908s ........................................................................ [ 87%] 2909s ......................................... [ 87%] 2913s testsuite/MDAnalysisTests/topology/test_lammpsdata.py .................. [ 87%] 2914s ........................................................................ [ 88%] 2914s ........................................................... [ 88%] 2914s testsuite/MDAnalysisTests/topology/test_minimal.py ..................... [ 88%] 2914s ........... [ 88%] 2915s testsuite/MDAnalysisTests/topology/test_mmtf.py ........................ [ 88%] 2915s .............................................. [ 88%] 2915s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%] 2915s ........ [ 89%] 2918s testsuite/MDAnalysisTests/topology/test_pdb.py ......................... [ 89%] 2919s ........................... [ 89%] 2919s testsuite/MDAnalysisTests/topology/test_pdbqt.py .......... [ 89%] 2920s testsuite/MDAnalysisTests/topology/test_pqr.py ........................ [ 89%] 2925s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%] 2928s ........................................ [ 89%] 2928s testsuite/MDAnalysisTests/topology/test_tables.py . [ 89%] 2929s testsuite/MDAnalysisTests/topology/test_top.py ......................... [ 90%] 2933s ........................................................................ [ 90%] 2934s ........................................................................ [ 90%] 2934s ........... [ 90%] 2934s testsuite/MDAnalysisTests/topology/test_topology_base.py ... [ 90%] 2934s testsuite/MDAnalysisTests/topology/test_topology_str_types.py .......... [ 90%] 2942s ........................................................................ [ 91%] 2943s .................. [ 91%] 2948s testsuite/MDAnalysisTests/topology/test_tprparser.py ................... [ 91%] 2955s ........................................................................ [ 91%] 2963s ........................................................................ [ 92%] 2971s ........................................................................ [ 92%] 2978s ........................................................................ [ 92%] 2988s ........................................................................ [ 93%] 2988s ........................................................................ [ 93%] 2988s ........................................................................ [ 93%] 2988s ........................................................................ [ 94%] 2988s ........................................................................ [ 94%] 2989s ........................................................................ [ 95%] 2989s ........................................................................ [ 95%] 2990s ........................................................................ [ 95%] 2992s .................................... [ 95%] 2992s testsuite/MDAnalysisTests/topology/test_txyz.py ....................... [ 96%] 2992s testsuite/MDAnalysisTests/topology/test_xpdb.py .......... [ 96%] 2992s testsuite/MDAnalysisTests/topology/test_xyz.py ......................... [ 96%] 2992s ... [ 96%] 2993s testsuite/MDAnalysisTests/transformations/test_base.py ..... [ 96%] 2993s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%] 2993s ...... [ 96%] 2993s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%] 2993s ......................................... [ 96%] 2994s testsuite/MDAnalysisTests/transformations/test_nojump.py ............ [ 96%] 2994s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%] 2994s . [ 96%] 2994s testsuite/MDAnalysisTests/transformations/test_rotate.py ............... [ 96%] 2994s ............................ [ 97%] 2994s testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%] 2994s ............ [ 97%] 3003s testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%] 3003s ....... [ 97%] 3003s testsuite/MDAnalysisTests/utils/test_authors.py . [ 97%] 3003s testsuite/MDAnalysisTests/utils/test_datafiles.py .... [ 97%] 3003s testsuite/MDAnalysisTests/utils/test_duecredit.py ........... [ 97%] 3003s testsuite/MDAnalysisTests/utils/test_failure.py . [ 97%] 3003s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%] 3003s ........................................................................ [ 97%] 3003s ........................................................................ [ 98%] 3003s ............................................. [ 98%] 3003s testsuite/MDAnalysisTests/utils/test_log.py . [ 98%] 3003s testsuite/MDAnalysisTests/utils/test_meta.py .... [ 98%] 3004s testsuite/MDAnalysisTests/utils/test_modelling.py ............. [ 98%] 3005s testsuite/MDAnalysisTests/utils/test_persistence.py ....... [ 98%] 3017s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%] 3017s ..............ss.. [ 98%] 3017s testsuite/MDAnalysisTests/utils/test_qcprot.py ...... [ 98%] 3019s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%] 3019s [ 98%] 3019s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 99%] 3019s ............... [ 99%] 3019s testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%] 3020s ........................................................................ [ 99%] 3020s ........................................................ [ 99%] 3020s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%] 3020s ....... [ 99%] 3020s testsuite/MDAnalysisTests/visualization/test_streamlines.py ... [100%] 3020s 3020s = 19104 passed, 558 skipped, 2 deselected, 7 xfailed, 2 xpassed, 104648 warnings in 1636.10s (0:27:16) = 3021s 3021s DueCredit Report: 3021s - Molecular simulation analysis library / MDAnalysis (v 2.8.0) [1, 2] 3021s - Iterative Calculation of Opimal Reference / MDAnalysis.analysis.align.iterative_average (v 2.8.0) [3] 3021s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.8.0) [4] 3021s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.8.0) [5] 3021s - DSSP algorithm description / MDAnalysis.analysis.dssp (v 2.8.0) [6] 3021s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.8.0) [7] 3021s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.8.0) [8] 3021s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.8.0) [9] 3021s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.8.0) [2] 3021s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.8.0) [10, 11] 3021s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.8.0) [12] 3021s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.8.0) [13, 14] 3021s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.8.0) [15] 3021s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.8.0) [16] 3021s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.8.0) [17, 18] 3021s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.8.0) [15] 3021s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.8.0) [19] 3021s - Scientific tools library / numpy (v 1.26.4) [20] 3021s 3021s 2 packages cited 3021s 16 modules cited 3021s 0 functions cited 3021s 3021s References 3021s ---------- 3021s 3021s [1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy. SciPy, pp. 98–105. 3021s [2] Michaud‐Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327. 3021s [3] Linke, M., Köfinger, J. & Hummer, G., 2018. Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 122(21), pp.5630–5639. 3021s [4] Minh, D.D.L., 2019. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. Journal of Computational Chemistry, 41(7), pp.715–730. 3021s [5] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 3021s [6] Kabsch, W. & Sander, C., 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers, 22(12), pp.2577–2637. 3021s [7] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 3021s [8] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857. 3021s [9] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22). 3021s [10] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877. 3021s [11] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232. 3021s [12] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330. 3021s [13] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy. SciPy, pp. 40–48. 3021s [14] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553. 3021s [15] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575. 3021s [16] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269. 3021s [17] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480. 3021s [18] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563. 3021s [19] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171. 3021s [20] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. 3025s autopkgtest [12:52:56]: test test-mdanalysis: -----------------------] 3030s autopkgtest [12:53:01]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 3030s test-mdanalysis PASS 3034s autopkgtest [12:53:05]: @@@@@@@@@@@@@@@@@@@@ summary 3034s test-mdanalysis PASS