0s autopkgtest [20:40:42]: starting date and time: 2024-11-23 20:40:42+0000 0s autopkgtest [20:40:42]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:40:42]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cbfkjsye/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:rdkit --apt-upgrade rdkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=rdkit/202309.3-7 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-17.secgroup --name adt-plucky-arm64-rdkit-20241123-204041-juju-7f2275-prod-proposed-migration-environment-15-997c453a-f89c-4751-89d9-2268365f540a --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 67s autopkgtest [20:41:49]: testbed dpkg architecture: arm64 67s autopkgtest [20:41:49]: testbed apt version: 2.9.8 67s autopkgtest [20:41:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [53.2 kB] 69s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 69s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [925 kB] 69s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 69s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [85.2 kB] 69s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 69s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [790 kB] 69s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [19.3 kB] 69s Fetched 2028 kB in 1s (2140 kB/s) 69s Reading package lists... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s Calculating upgrade... 73s The following package was automatically installed and is no longer required: 73s libsgutils2-1.46-2 73s Use 'sudo apt autoremove' to remove it. 73s The following NEW packages will be installed: 73s libsgutils2-1.48 73s The following packages will be upgraded: 73s bash bpftrace curl debconf debconf-i18n distro-info dracut-install 73s fwupd-signed gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname 73s libaudit-common libaudit1 libcurl3t64-gnutls libcurl4t64 73s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libpam-modules 73s libpam-modules-bin libpam-runtime libpam0g libplymouth5 libselinux1 73s libsemanage-common libsemanage2 linux-base lxd-installer openssh-client 73s openssh-server openssh-sftp-server pinentry-curses plymouth 73s plymouth-theme-ubuntu-text python3-blinker python3-dbus python3-debconf 73s python3-gi python3-jsonschema-specifications python3-rpds-py python3-yaml 73s sg3-utils sg3-utils-udev vim-common vim-tiny xxd 73s 46 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 73s Need to get 11.7 MB of archives. 73s After this operation, 2984 kB of additional disk space will be used. 73s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 bash arm64 5.2.32-1ubuntu2 [791 kB] 74s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 hostname arm64 3.25 [11.0 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B] 74s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libaudit1 arm64 1:4.0.2-2ubuntu1 [54.2 kB] 74s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 debconf-i18n all 1.5.87ubuntu1 [204 kB] 74s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-debconf all 1.5.87ubuntu1 [4156 B] 74s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 debconf all 1.5.87ubuntu1 [124 kB] 74s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam0g arm64 1.5.3-7ubuntu4 [68.6 kB] 74s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libselinux1 arm64 3.7-3ubuntu1 [81.6 kB] 74s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam-modules-bin arm64 1.5.3-7ubuntu4 [50.4 kB] 74s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam-modules arm64 1.5.3-7ubuntu4 [285 kB] 74s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 openssh-sftp-server arm64 1:9.9p1-3ubuntu2 [36.8 kB] 74s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 openssh-server arm64 1:9.9p1-3ubuntu2 [524 kB] 74s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 openssh-client arm64 1:9.9p1-3ubuntu2 [920 kB] 74s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB] 74s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libsemanage-common all 3.7-2build1 [7186 B] 74s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libsemanage2 arm64 3.7-2build1 [92.2 kB] 74s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 distro-info arm64 1.12 [19.4 kB] 74s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-girepository-2.0 arm64 1.82.0-2 [25.2 kB] 74s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-glib-2.0 arm64 2.82.2-3 [182 kB] 74s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1560 kB] 74s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgirepository-1.0-1 arm64 1.82.0-2 [83.0 kB] 74s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-data all 2.82.2-3 [51.7 kB] 74s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dbus arm64 1.3.2-5build4 [109 kB] 74s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-gi arm64 3.50.0-3build1 [279 kB] 74s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-yaml arm64 6.0.2-1build1 [164 kB] 74s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-tiny arm64 2:9.1.0861-1ubuntu1 [805 kB] 74s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 74s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 xxd arm64 2:9.1.0861-1ubuntu1 [67.3 kB] 74s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libplymouth5 arm64 24.004.60-2ubuntu3 [141 kB] 74s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60-2ubuntu3 [9914 B] 74s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 plymouth arm64 24.004.60-2ubuntu3 [135 kB] 74s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 bpftrace arm64 0.21.2-2ubuntu3 [1854 kB] 74s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 curl arm64 8.9.1-2ubuntu3 [235 kB] 74s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl4t64 arm64 8.9.1-2ubuntu3 [365 kB] 74s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 dracut-install arm64 105-2ubuntu2 [34.7 kB] 74s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 fwupd-signed arm64 1.55+1.7-1 [30.9 kB] 74s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl3t64-gnutls arm64 8.9.1-2ubuntu3 [359 kB] 74s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libsgutils2-1.48 arm64 1.48-0ubuntu1 [118 kB] 74s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 linux-base all 4.10.1ubuntu1 [34.8 kB] 74s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 lxd-installer all 10 [5264 B] 74s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-0ubuntu2 [38.5 kB] 74s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-blinker all 1.9.0-1 [10.7 kB] 74s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-rpds-py arm64 0.21.0-2ubuntu1 [302 kB] 74s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B] 74s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 sg3-utils arm64 1.48-0ubuntu1 [999 kB] 75s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B] 75s Preconfiguring packages ... 75s Fetched 11.7 MB in 1s (9932 kB/s) 75s (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 ... 80002 files and directories currently installed.) 75s Preparing to unpack .../bash_5.2.32-1ubuntu2_arm64.deb ... 75s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 75s Setting up bash (5.2.32-1ubuntu2) ... 75s 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 75s (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 ... 80002 files and directories currently installed.) 75s Preparing to unpack .../hostname_3.25_arm64.deb ... 75s Unpacking hostname (3.25) over (3.23+nmu2ubuntu2) ... 76s Setting up hostname (3.25) ... 76s (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 ... 80002 files and directories currently installed.) 76s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu1_all.deb ... 76s Unpacking libaudit-common (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 76s Setting up libaudit-common (1:4.0.2-2ubuntu1) ... 76s (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 ... 80002 files and directories currently installed.) 76s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu1_arm64.deb ... 76s Unpacking libaudit1:arm64 (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 76s Setting up libaudit1:arm64 (1:4.0.2-2ubuntu1) ... 76s (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 ... 80002 files and directories currently installed.) 76s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 76s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 76s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 76s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 76s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 76s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 76s Setting up debconf (1.5.87ubuntu1) ... 76s (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 ... 80002 files and directories currently installed.) 76s Preparing to unpack .../libpam0g_1.5.3-7ubuntu4_arm64.deb ... 76s Unpacking libpam0g:arm64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 76s Setting up libpam0g:arm64 (1.5.3-7ubuntu4) ... 76s (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 ... 80002 files and directories currently installed.) 76s Preparing to unpack .../libselinux1_3.7-3ubuntu1_arm64.deb ... 76s Unpacking libselinux1:arm64 (3.7-3ubuntu1) over (3.5-2ubuntu5) ... 77s Setting up libselinux1:arm64 (3.7-3ubuntu1) ... 77s (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 ... 80002 files and directories currently installed.) 77s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu4_arm64.deb ... 77s Unpacking libpam-modules-bin (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 77s Setting up libpam-modules-bin (1.5.3-7ubuntu4) ... 77s pam_namespace.service is a disabled or a static unit not running, not starting it. 77s (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 ... 80002 files and directories currently installed.) 77s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu4_arm64.deb ... 77s Unpacking libpam-modules:arm64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 77s Setting up libpam-modules:arm64 (1.5.3-7ubuntu4) ... 77s (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 ... 80002 files and directories currently installed.) 77s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_arm64.deb ... 77s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 77s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_arm64.deb ... 77s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 77s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_arm64.deb ... 77s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 78s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ... 78s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 78s Setting up libpam-runtime (1.5.3-7ubuntu4) ... 78s (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 ... 80004 files and directories currently installed.) 78s Preparing to unpack .../libsemanage-common_3.7-2build1_all.deb ... 78s Unpacking libsemanage-common (3.7-2build1) over (3.5-1build6) ... 78s Setting up libsemanage-common (3.7-2build1) ... 78s (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 ... 80003 files and directories currently installed.) 78s Preparing to unpack .../libsemanage2_3.7-2build1_arm64.deb ... 78s Unpacking libsemanage2:arm64 (3.7-2build1) over (3.5-1build6) ... 78s Setting up libsemanage2:arm64 (3.7-2build1) ... 78s (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 ... 80003 files and directories currently installed.) 78s Preparing to unpack .../00-distro-info_1.12_arm64.deb ... 78s Unpacking distro-info (1.12) over (1.9) ... 78s Preparing to unpack .../01-gir1.2-girepository-2.0_1.82.0-2_arm64.deb ... 78s Unpacking gir1.2-girepository-2.0:arm64 (1.82.0-2) over (1.80.1-4) ... 78s Preparing to unpack .../02-gir1.2-glib-2.0_2.82.2-3_arm64.deb ... 78s Unpacking gir1.2-glib-2.0:arm64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 78s Preparing to unpack .../03-libglib2.0-0t64_2.82.2-3_arm64.deb ... 78s Unpacking libglib2.0-0t64:arm64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 78s Preparing to unpack .../04-libgirepository-1.0-1_1.82.0-2_arm64.deb ... 78s Unpacking libgirepository-1.0-1:arm64 (1.82.0-2) over (1.80.1-4) ... 78s Preparing to unpack .../05-libglib2.0-data_2.82.2-3_all.deb ... 78s Unpacking libglib2.0-data (2.82.2-3) over (2.82.1-0ubuntu1) ... 78s Preparing to unpack .../06-python3-dbus_1.3.2-5build4_arm64.deb ... 78s Unpacking python3-dbus (1.3.2-5build4) over (1.3.2-5build3) ... 78s Preparing to unpack .../07-python3-gi_3.50.0-3build1_arm64.deb ... 79s Unpacking python3-gi (3.50.0-3build1) over (3.50.0-3) ... 79s Preparing to unpack .../08-python3-yaml_6.0.2-1build1_arm64.deb ... 79s Unpacking python3-yaml (6.0.2-1build1) over (6.0.2-1) ... 79s Preparing to unpack .../09-vim-tiny_2%3a9.1.0861-1ubuntu1_arm64.deb ... 79s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 79s Preparing to unpack .../10-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 79s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 79s Preparing to unpack .../11-xxd_2%3a9.1.0861-1ubuntu1_arm64.deb ... 79s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 79s Preparing to unpack .../12-libplymouth5_24.004.60-2ubuntu3_arm64.deb ... 79s Unpacking libplymouth5:arm64 (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 79s Preparing to unpack .../13-plymouth-theme-ubuntu-text_24.004.60-2ubuntu3_arm64.deb ... 79s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 79s Preparing to unpack .../14-plymouth_24.004.60-2ubuntu3_arm64.deb ... 79s Unpacking plymouth (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 79s Preparing to unpack .../15-bpftrace_0.21.2-2ubuntu3_arm64.deb ... 79s Unpacking bpftrace (0.21.2-2ubuntu3) over (0.21.2-2ubuntu2) ... 79s Preparing to unpack .../16-curl_8.9.1-2ubuntu3_arm64.deb ... 79s Unpacking curl (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 79s Preparing to unpack .../17-libcurl4t64_8.9.1-2ubuntu3_arm64.deb ... 79s Unpacking libcurl4t64:arm64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 79s Preparing to unpack .../18-dracut-install_105-2ubuntu2_arm64.deb ... 79s Unpacking dracut-install (105-2ubuntu2) over (105-1ubuntu1) ... 79s Preparing to unpack .../19-fwupd-signed_1.55+1.7-1_arm64.deb ... 79s Unpacking fwupd-signed (1.55+1.7-1) over (1.54+1.6-1build1) ... 79s Preparing to unpack .../20-libcurl3t64-gnutls_8.9.1-2ubuntu3_arm64.deb ... 79s Unpacking libcurl3t64-gnutls:arm64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 79s Selecting previously unselected package libsgutils2-1.48:arm64. 79s Preparing to unpack .../21-libsgutils2-1.48_1.48-0ubuntu1_arm64.deb ... 79s Unpacking libsgutils2-1.48:arm64 (1.48-0ubuntu1) ... 79s Preparing to unpack .../22-linux-base_4.10.1ubuntu1_all.deb ... 79s Unpacking linux-base (4.10.1ubuntu1) over (4.5ubuntu9) ... 79s Preparing to unpack .../23-lxd-installer_10_all.deb ... 79s Unpacking lxd-installer (10) over (9) ... 79s Preparing to unpack .../24-pinentry-curses_1.3.1-0ubuntu2_arm64.deb ... 79s Unpacking pinentry-curses (1.3.1-0ubuntu2) over (1.2.1-3ubuntu5) ... 80s Preparing to unpack .../25-python3-blinker_1.9.0-1_all.deb ... 80s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 80s Preparing to unpack .../26-python3-rpds-py_0.21.0-2ubuntu1_arm64.deb ... 80s Unpacking python3-rpds-py (0.21.0-2ubuntu1) over (0.20.0-0ubuntu3) ... 80s Preparing to unpack .../27-python3-jsonschema-specifications_2023.12.1-2_all.deb ... 80s Unpacking python3-jsonschema-specifications (2023.12.1-2) over (2023.12.1-1ubuntu1) ... 80s Preparing to unpack .../28-sg3-utils_1.48-0ubuntu1_arm64.deb ... 80s Unpacking sg3-utils (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 80s Preparing to unpack .../29-sg3-utils-udev_1.48-0ubuntu1_all.deb ... 80s Unpacking sg3-utils-udev (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 80s Setting up pinentry-curses (1.3.1-0ubuntu2) ... 80s Setting up distro-info (1.12) ... 80s Setting up linux-base (4.10.1ubuntu1) ... 80s Setting up libcurl4t64:arm64 (8.9.1-2ubuntu3) ... 80s Setting up bpftrace (0.21.2-2ubuntu3) ... 80s Setting up openssh-client (1:9.9p1-3ubuntu2) ... 80s Setting up python3-debconf (1.5.87ubuntu1) ... 80s Setting up libcurl3t64-gnutls:arm64 (8.9.1-2ubuntu3) ... 80s Setting up fwupd-signed (1.55+1.7-1) ... 80s Setting up libsgutils2-1.48:arm64 (1.48-0ubuntu1) ... 80s Setting up python3-yaml (6.0.2-1build1) ... 80s Setting up debconf-i18n (1.5.87ubuntu1) ... 80s Setting up xxd (2:9.1.0861-1ubuntu1) ... 80s Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... 80s No schema files found: doing nothing. 80s Setting up libglib2.0-data (2.82.2-3) ... 80s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 80s Setting up gir1.2-glib-2.0:arm64 (2.82.2-3) ... 80s Setting up lxd-installer (10) ... 81s Setting up python3-rpds-py (0.21.0-2ubuntu1) ... 81s Setting up dracut-install (105-2ubuntu2) ... 81s Setting up libplymouth5:arm64 (24.004.60-2ubuntu3) ... 81s Setting up libgirepository-1.0-1:arm64 (1.82.0-2) ... 81s Setting up curl (8.9.1-2ubuntu3) ... 81s Setting up python3-jsonschema-specifications (2023.12.1-2) ... 81s Setting up sg3-utils (1.48-0ubuntu1) ... 81s Setting up python3-blinker (1.9.0-1) ... 81s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ... 81s Setting up python3-dbus (1.3.2-5build4) ... 81s Setting up openssh-server (1:9.9p1-3ubuntu2) ... 81s Installing new version of config file /etc/ssh/moduli ... 82s Replacing config file /etc/ssh/sshd_config with new version 83s Setting up plymouth (24.004.60-2ubuntu3) ... 83s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 83s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 98s flash-kernel: deferring update (trigger activated) 98s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 99s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 99s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 99s Setting up sg3-utils-udev (1.48-0ubuntu1) ... 99s update-initramfs: deferring update (trigger activated) 99s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ... 99s update-initramfs: deferring update (trigger activated) 99s Setting up gir1.2-girepository-2.0:arm64 (1.82.0-2) ... 99s Setting up python3-gi (3.50.0-3build1) ... 99s Processing triggers for install-info (7.1.1-1) ... 99s Processing triggers for initramfs-tools (0.142ubuntu35) ... 99s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 99s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 113s System running in EFI mode, skipping. 113s Processing triggers for libc-bin (2.40-1ubuntu3) ... 113s Processing triggers for ufw (0.36.2-8) ... 113s Processing triggers for man-db (2.13.0-1) ... 115s Processing triggers for debianutils (5.21) ... 115s Processing triggers for flash-kernel (3.107ubuntu13) ... 115s System running in EFI mode, skipping. 115s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s The following packages will be REMOVED: 116s libsgutils2-1.46-2* 117s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 117s After this operation, 314 kB disk space will be freed. 117s (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 ... 80037 files and directories currently installed.) 117s Removing libsgutils2-1.46-2:arm64 (1.46-3ubuntu5) ... 117s Processing triggers for libc-bin (2.40-1ubuntu3) ... 117s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 117s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 117s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 117s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 118s Reading package lists... 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s autopkgtest [20:42:43]: rebooting testbed after setup commands that affected boot 125s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 147s autopkgtest [20:43:09]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 150s autopkgtest [20:43:12]: @@@@@@@@@@@@@@@@@@@@ apt-source rdkit 159s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe rdkit 202309.3-7 (dsc) [2959 B] 159s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe rdkit 202309.3-7 (tar) [61.9 MB] 159s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe rdkit 202309.3-7 (diff) [25.2 kB] 159s gpgv: Signature made Mon Sep 23 11:07:49 2024 UTC 159s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 159s gpgv: issuer "merkys@debian.org" 159s gpgv: Can't check signature: No public key 159s dpkg-source: warning: cannot verify inline signature for ./rdkit_202309.3-7.dsc: no acceptable signature found 162s autopkgtest [20:43:24]: testing package rdkit version 202309.3-7 162s autopkgtest [20:43:24]: build not needed 171s autopkgtest [20:43:33]: test installcheck: preparing testbed 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 182s The following additional packages will be installed: 182s fontconfig-config fonts-freefont-ttf libblas3 libboost-iostreams1.83.0 182s libboost-python1.83.0 libboost-serialization1.83.0 libcairo2 libcoordgen3 182s libfontconfig1 libgfortran5 libinchi1.07 libjs-jquery libjs-underscore 182s libjson-perl liblapack3 libmaeparser1 libpixman-1-0 libpq5 librdkit-dev 182s librdkit1t64 libxcb-render0 libxcb-shm0 libxrender1 libxslt1.1 postgresql-17 182s postgresql-17-rdkit postgresql-client-17 postgresql-client-common 182s postgresql-common python3-numpy python3-rdkit rdkit-data rdkit-doc ssl-cert 182s Suggested packages: 182s postgresql-doc-17 gcc gfortran python-numpy-doc python3-dev python3-pytest 182s Recommended packages: 182s javascript-common libjson-xs-perl 182s The following NEW packages will be installed: 182s autopkgtest-satdep fontconfig-config fonts-freefont-ttf libblas3 182s libboost-iostreams1.83.0 libboost-python1.83.0 libboost-serialization1.83.0 182s libcairo2 libcoordgen3 libfontconfig1 libgfortran5 libinchi1.07 libjs-jquery 182s libjs-underscore libjson-perl liblapack3 libmaeparser1 libpixman-1-0 libpq5 182s librdkit-dev librdkit1t64 libxcb-render0 libxcb-shm0 libxrender1 libxslt1.1 182s postgresql-17 postgresql-17-rdkit postgresql-client-17 182s postgresql-client-common postgresql-common python3-numpy python3-rdkit 182s rdkit-data rdkit-doc ssl-cert 182s 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. 182s Need to get 65.0 MB/65.0 MB of archives. 182s After this operation, 336 MB of additional disk space will be used. 182s Get:1 /tmp/autopkgtest.sGFASs/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [756 B] 182s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-client-common all 262 [36.7 kB] 183s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 ssl-cert all 1.1.3ubuntu1 [18.7 kB] 183s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-common all 262 [162 kB] 183s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 183s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 183s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 183s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-iostreams1.83.0 arm64 1.83.0-3.2ubuntu2 [259 kB] 183s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-python1.83.0 arm64 1.83.0-3.2ubuntu2 [307 kB] 183s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libboost-serialization1.83.0 arm64 1.83.0-3.2ubuntu2 [338 kB] 183s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 183s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 183s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 183s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 183s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 183s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 183s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcoordgen3 arm64 3.0.2-1 [207 kB] 183s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 183s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libinchi1.07 arm64 1.07.1+dfsg-5 [574 kB] 183s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 183s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 183s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 183s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmaeparser1 arm64 1.3.1-1build1 [84.5 kB] 183s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libpq5 arm64 17.0-1 [248 kB] 183s Get:26 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit1t64 arm64 202309.3-7 [4929 kB] 184s Get:27 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 librdkit-dev arm64 202309.3-7 [305 kB] 184s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 184s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-client-17 arm64 17.0-1 [2102 kB] 184s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 postgresql-17 arm64 17.0-1 [17.7 MB] 184s Get:31 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 postgresql-17-rdkit arm64 202309.3-7 [358 kB] 184s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 184s Get:33 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-data all 202309.3-7 [12.6 MB] 185s Get:34 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-rdkit arm64 202309.3-7 [4647 kB] 185s Get:35 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 rdkit-doc all 202309.3-7 [5829 kB] 185s Preconfiguring packages ... 186s Fetched 65.0 MB in 3s (22.9 MB/s) 186s Selecting previously unselected package libjson-perl. 186s (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 ... 80032 files and directories currently installed.) 186s Preparing to unpack .../00-libjson-perl_4.10000-1_all.deb ... 186s Unpacking libjson-perl (4.10000-1) ... 186s Selecting previously unselected package postgresql-client-common. 186s Preparing to unpack .../01-postgresql-client-common_262_all.deb ... 186s Unpacking postgresql-client-common (262) ... 186s Selecting previously unselected package ssl-cert. 186s Preparing to unpack .../02-ssl-cert_1.1.3ubuntu1_all.deb ... 186s Unpacking ssl-cert (1.1.3ubuntu1) ... 186s Selecting previously unselected package postgresql-common. 186s Preparing to unpack .../03-postgresql-common_262_all.deb ... 186s Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by postgresql-common' 186s Unpacking postgresql-common (262) ... 186s Selecting previously unselected package fonts-freefont-ttf. 186s Preparing to unpack .../04-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 186s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 186s Selecting previously unselected package fontconfig-config. 186s Preparing to unpack .../05-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 186s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 186s Selecting previously unselected package libblas3:arm64. 186s Preparing to unpack .../06-libblas3_3.12.0-3build2_arm64.deb ... 186s Unpacking libblas3:arm64 (3.12.0-3build2) ... 186s Selecting previously unselected package libboost-iostreams1.83.0:arm64. 186s Preparing to unpack .../07-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_arm64.deb ... 186s Unpacking libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ... 186s Selecting previously unselected package libboost-python1.83.0. 186s Preparing to unpack .../08-libboost-python1.83.0_1.83.0-3.2ubuntu2_arm64.deb ... 186s Unpacking libboost-python1.83.0 (1.83.0-3.2ubuntu2) ... 186s Selecting previously unselected package libboost-serialization1.83.0:arm64. 187s Preparing to unpack .../09-libboost-serialization1.83.0_1.83.0-3.2ubuntu2_arm64.deb ... 187s Unpacking libboost-serialization1.83.0:arm64 (1.83.0-3.2ubuntu2) ... 187s Selecting previously unselected package libfontconfig1:arm64. 187s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 187s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 187s Selecting previously unselected package libpixman-1-0:arm64. 187s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_arm64.deb ... 187s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 187s Selecting previously unselected package libxcb-render0:arm64. 187s Preparing to unpack .../12-libxcb-render0_1.17.0-2_arm64.deb ... 187s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 187s Selecting previously unselected package libxcb-shm0:arm64. 187s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_arm64.deb ... 187s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 187s Selecting previously unselected package libxrender1:arm64. 187s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 187s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 187s Selecting previously unselected package libcairo2:arm64. 187s Preparing to unpack .../15-libcairo2_1.18.2-2_arm64.deb ... 187s Unpacking libcairo2:arm64 (1.18.2-2) ... 187s Selecting previously unselected package libcoordgen3:arm64. 187s Preparing to unpack .../16-libcoordgen3_3.0.2-1_arm64.deb ... 187s Unpacking libcoordgen3:arm64 (3.0.2-1) ... 187s Selecting previously unselected package libgfortran5:arm64. 187s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 187s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 187s Selecting previously unselected package libinchi1.07. 187s Preparing to unpack .../18-libinchi1.07_1.07.1+dfsg-5_arm64.deb ... 187s Unpacking libinchi1.07 (1.07.1+dfsg-5) ... 187s Selecting previously unselected package libjs-jquery. 187s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 187s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 187s Selecting previously unselected package libjs-underscore. 187s Preparing to unpack .../20-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 187s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 187s Selecting previously unselected package liblapack3:arm64. 187s Preparing to unpack .../21-liblapack3_3.12.0-3build2_arm64.deb ... 187s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 187s Selecting previously unselected package libmaeparser1:arm64. 187s Preparing to unpack .../22-libmaeparser1_1.3.1-1build1_arm64.deb ... 187s Unpacking libmaeparser1:arm64 (1.3.1-1build1) ... 187s Selecting previously unselected package libpq5:arm64. 187s Preparing to unpack .../23-libpq5_17.0-1_arm64.deb ... 187s Unpacking libpq5:arm64 (17.0-1) ... 187s Selecting previously unselected package librdkit1t64. 187s Preparing to unpack .../24-librdkit1t64_202309.3-7_arm64.deb ... 187s Unpacking librdkit1t64 (202309.3-7) ... 187s Selecting previously unselected package librdkit-dev. 187s Preparing to unpack .../25-librdkit-dev_202309.3-7_arm64.deb ... 187s Unpacking librdkit-dev (202309.3-7) ... 187s Selecting previously unselected package libxslt1.1:arm64. 187s Preparing to unpack .../26-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 187s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 187s Selecting previously unselected package postgresql-client-17. 187s Preparing to unpack .../27-postgresql-client-17_17.0-1_arm64.deb ... 187s Unpacking postgresql-client-17 (17.0-1) ... 188s Selecting previously unselected package postgresql-17. 188s Preparing to unpack .../28-postgresql-17_17.0-1_arm64.deb ... 188s Unpacking postgresql-17 (17.0-1) ... 188s Selecting previously unselected package postgresql-17-rdkit. 188s Preparing to unpack .../29-postgresql-17-rdkit_202309.3-7_arm64.deb ... 188s Unpacking postgresql-17-rdkit (202309.3-7) ... 188s Selecting previously unselected package python3-numpy. 188s Preparing to unpack .../30-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 188s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 188s Selecting previously unselected package rdkit-data. 188s Preparing to unpack .../31-rdkit-data_202309.3-7_all.deb ... 188s Unpacking rdkit-data (202309.3-7) ... 189s Selecting previously unselected package python3-rdkit. 189s Preparing to unpack .../32-python3-rdkit_202309.3-7_arm64.deb ... 189s Unpacking python3-rdkit (202309.3-7) ... 189s Selecting previously unselected package rdkit-doc. 189s Preparing to unpack .../33-rdkit-doc_202309.3-7_all.deb ... 189s Unpacking rdkit-doc (202309.3-7) ... 189s Selecting previously unselected package autopkgtest-satdep. 189s Preparing to unpack .../34-1-autopkgtest-satdep.deb ... 189s Unpacking autopkgtest-satdep (0) ... 190s Setting up postgresql-client-common (262) ... 190s Setting up libboost-python1.83.0 (1.83.0-3.2ubuntu2) ... 190s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 190s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 190s Setting up libxcb-render0:arm64 (1.17.0-2) ... 190s Setting up libpq5:arm64 (17.0-1) ... 190s Setting up fonts-freefont-ttf (20211204+svn4273-2) ... 190s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 190s Setting up rdkit-data (202309.3-7) ... 190s Setting up libboost-serialization1.83.0:arm64 (1.83.0-3.2ubuntu2) ... 190s Setting up libblas3:arm64 (3.12.0-3build2) ... 190s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 190s Setting up ssl-cert (1.1.3ubuntu1) ... 190s Created symlink '/etc/systemd/system/multi-user.target.wants/ssl-cert.service' → '/usr/lib/systemd/system/ssl-cert.service'. 190s Setting up libboost-iostreams1.83.0:arm64 (1.83.0-3.2ubuntu2) ... 190s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 190s Setting up libjson-perl (4.10000-1) ... 190s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 190s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 190s Setting up libcoordgen3:arm64 (3.0.2-1) ... 190s Setting up libinchi1.07 (1.07.1+dfsg-5) ... 190s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 190s Setting up liblapack3:arm64 (3.12.0-3build2) ... 190s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 190s Setting up postgresql-client-17 (17.0-1) ... 191s update-alternatives: using /usr/share/postgresql/17/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode 191s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 191s Setting up rdkit-doc (202309.3-7) ... 191s Setting up libmaeparser1:arm64 (1.3.1-1build1) ... 191s Setting up postgresql-common (262) ... 191s 191s Creating config file /etc/postgresql-common/createcluster.conf with new version 192s Building PostgreSQL dictionaries from installed myspell/hunspell packages... 192s Removing obsolete dictionary files: 192s Created symlink '/etc/systemd/system/multi-user.target.wants/postgresql.service' → '/usr/lib/systemd/system/postgresql.service'. 193s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 195s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 195s Setting up postgresql-17 (17.0-1) ... 195s Creating new PostgreSQL cluster 17/main ... 195s /usr/lib/postgresql/17/bin/initdb -D /var/lib/postgresql/17/main --auth-local peer --auth-host scram-sha-256 --no-instructions 195s The files belonging to this database system will be owned by user "postgres". 195s This user must also own the server process. 195s 195s The database cluster will be initialized with locale "C.UTF-8". 195s The default database encoding has accordingly been set to "UTF8". 195s The default text search configuration will be set to "english". 195s 195s Data page checksums are disabled. 195s 195s fixing permissions on existing directory /var/lib/postgresql/17/main ... ok 195s creating subdirectories ... ok 195s selecting dynamic shared memory implementation ... posix 195s selecting default "max_connections" ... 100 195s selecting default "shared_buffers" ... 128MB 195s selecting default time zone ... Etc/UTC 195s creating configuration files ... ok 195s running bootstrap script ... ok 196s performing post-bootstrap initialization ... ok 196s syncing data to disk ... ok 199s Setting up libcairo2:arm64 (1.18.2-2) ... 199s Setting up librdkit1t64 (202309.3-7) ... 199s Setting up postgresql-17-rdkit (202309.3-7) ... 199s Setting up python3-rdkit (202309.3-7) ... 200s Setting up librdkit-dev (202309.3-7) ... 200s Setting up autopkgtest-satdep (0) ... 200s Processing triggers for man-db (2.13.0-1) ... 201s Processing triggers for libc-bin (2.40-1ubuntu3) ... 206s (Reading database ... 89632 files and directories currently installed.) 206s Removing autopkgtest-satdep (0) ... 206s autopkgtest [20:44:08]: test installcheck: [----------------------- 206s ### PostgreSQL 17 installcheck ### 207s Creating new PostgreSQL cluster 17/regress ... 209s make: Entering directory '/tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit' 209s echo "# +++ regress install-check in +++" && /usr/lib/postgresql/17/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=/tmp/autopkgtest.sGFASs/build.jmP/src --bindir='/usr/lib/postgresql/17/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 bfpgin sfpgist slfpgist fps reaction fmcs query xqm 209s # +++ regress install-check in +++ 209s # using postmaster on localhost, port 5433 210s not ok 1 - rdkit-91 115 ms 210s not ok 2 - props 25 ms 210s not ok 3 - btree 23 ms 210s not ok 4 - molgist 22 ms 210s not ok 5 - bfpgist-91 20 ms 210s not ok 6 - bfpgin 20 ms 210s not ok 7 - sfpgist 20 ms 210s not ok 8 - slfpgist 20 ms 210s not ok 9 - fps 22 ms 210s not ok 10 - reaction 38 ms 210s not ok 11 - fmcs 19 ms 210s not ok 12 - query 19 ms 210s not ok 13 - xqm 22 ms 210s 1..13 210s # 13 of 13 tests failed. 210s # The differences that caused some tests to fail can be viewed in the file "/tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/regression.diffs". 210s # A copy of the test summary that you see above is saved in the file "/tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/regression.out". 210s make: Leaving directory '/tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit' 210s make: *** [/usr/lib/postgresql/17/lib/pgxs/src/makefiles/pgxs.mk:436: installcheck] Error 1 210s *** /tmp/pg_virtualenv.Ci4Ber/log/postgresql-17-regress.log (last 100 lines) *** 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 18 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'CCCCOC'::mol@>mol_to_xqmol('CCCC'::mol); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 27 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'COC1=NNC(CC)=C1'::mol @>> mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}'); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 28 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'COC1=NNC(C=C)=C1'::mol @>> mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}'); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 27 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'COC1=NNC(CC)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 28 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'COC1=NNC(C=C)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 28 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'COOC1=NNC(CC)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 29 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'COOC1=NNC(C=C)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 54 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'CCOC(=O)c1cc2n(n1)C(C(=O)O)Nc1cc(Cl)ccc1-2'::mol @> mol_to_xqmol('COCc1n[nH]c(C)c1 |LN:1:1.3|'::mol); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 33 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'Cc1ccnc2nc(CN)[nH]c12'::mol@>>mol_to_xqmol(mol_from_ctab('qry 210s Mrv2305 09052314502D 210s 210s 0 0 0 0 0 999 V3000 210s M V30 BEGIN CTAB 210s M V30 COUNTS 13 13 0 0 0 210s M V30 BEGIN ATOM 210s M V30 1 N -4.75 1.9567 0 0 210s M V30 2 C -6.0837 1.1867 0 0 210s M V30 3 C -6.0837 -0.3534 0 0 210s M V30 4 C -4.75 -1.1234 0 0 210s M V30 5 C -3.4163 -0.3534 0 0 210s M V30 6 C -3.4163 1.1867 0 0 210s M V30 7 N -1.9692 1.7134 0 0 210s M V30 8 N -1.8822 -0.7768 0 0 210s M V30 9 C -1.0211 0.4999 0 0 210s M V30 10 C 0.5179 0.5536 0 0 210s M V30 11 N 1.2409 1.9133 0 0 210s M V30 12 * -5.6391 -0.0967 0 0 210s M V30 13 C -5.6391 -2.4067 0 0 210s M V30 END ATOM 210s M V30 BEGIN BOND 210s M V30 1 1 1 2 210s M V30 2 2 2 3 210s M V30 3 1 3 4 210s M V30 4 2 4 5 210s M V30 5 1 5 6 210s M V30 6 2 1 6 210s M V30 7 1 8 9 210s M V30 8 1 7 6 210s M V30 9 1 5 8 210s M V30 10 2 7 9 210s M V30 11 1 9 10 210s M V30 12 1 10 11 210s M V30 13 1 12 13 ENDPTS=(3 4 3 2) ATTACH=ANY 210s M V30 END BOND 210s M V30 END CTAB 210s M END')); 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression ERROR: type "mol" does not exist at character 32 210s 2024-11-23 20:44:12.446 UTC [4315] ubuntu@contrib_regression STATEMENT: select 'c1ccnc2nc(CN)[nH]c12'::mol@>>mol_to_xqmol(mol_from_ctab('qry 210s Mrv2305 09052314502D 210s 210s 0 0 0 0 0 999 V3000 210s M V30 BEGIN CTAB 210s M V30 COUNTS 13 13 0 0 0 210s M V30 BEGIN ATOM 210s M V30 1 N -4.75 1.9567 0 0 210s M V30 2 C -6.0837 1.1867 0 0 210s M V30 3 C -6.0837 -0.3534 0 0 210s M V30 4 C -4.75 -1.1234 0 0 210s M V30 5 C -3.4163 -0.3534 0 0 210s M V30 6 C -3.4163 1.1867 0 0 210s M V30 7 N -1.9692 1.7134 0 0 210s M V30 8 N -1.8822 -0.7768 0 0 210s M V30 9 C -1.0211 0.4999 0 0 210s M V30 10 C 0.5179 0.5536 0 0 210s M V30 11 N 1.2409 1.9133 0 0 210s M V30 12 * -5.6391 -0.0967 0 0 210s M V30 13 C -5.6391 -2.4067 0 0 210s M V30 END ATOM 210s M V30 BEGIN BOND 210s M V30 1 1 1 2 210s M V30 2 2 2 3 210s M V30 3 1 3 4 210s M V30 4 2 4 5 210s M V30 5 1 5 6 210s M V30 6 2 1 6 210s M V30 7 1 8 9 210s M V30 8 1 7 6 210s M V30 9 1 5 8 210s M V30 10 2 7 9 210s M V30 11 1 9 10 210s M V30 12 1 10 11 210s M V30 13 1 12 13 ENDPTS=(3 4 3 2) ATTACH=ANY 210s M V30 END BOND 210s M V30 END CTAB 210s M END')); 210s Dropping cluster 17/regress ... 210s **** /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/regression.diffs **** 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/rdkit-91_1.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/rdkit-91.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/rdkit-91_1.out 2024-11-23 20:43:25.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/rdkit-91.out 2024-11-23 20:44:12.099715940 +0000 210s @@ -4,181 +4,160 @@ 210s -- 210s SET client_min_messages = warning; 210s \set ECHO none 210s +ERROR: commutator operator = is already the commutator of operator = 210s RESET client_min_messages; 210s +SET extra_float_digits=0; 210s SELECT is_valid_smiles('c1ccccc1'); 210s - is_valid_smiles 210s ------------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: function is_valid_smiles(unknown) does not exist 210s +LINE 1: SELECT is_valid_smiles('c1ccccc1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_from_smiles('c1ccccc1'); 210s - mol_from_smiles 210s ------------------ 210s - c1ccccc1 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_from_smiles('c1ccccc1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT is_valid_smiles('c1ccccc'); 210s - is_valid_smiles 210s ------------------ 210s - f 210s -(1 row) 210s - 210s +ERROR: function is_valid_smiles(unknown) does not exist 210s +LINE 1: SELECT is_valid_smiles('c1ccccc'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_from_smiles('c1ccccc'); 210s -WARNING: could not create molecule from SMILES 'c1ccccc' 210s - mol_from_smiles 210s ------------------ 210s - 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_from_smiles('c1ccccc'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_from_smiles('cccccc'); 210s -WARNING: could not create molecule from SMILES 'cccccc' 210s - mol_from_smiles 210s ------------------ 210s - 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_from_smiles('cccccc'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT is_valid_smiles('c1cccn1'); 210s - is_valid_smiles 210s ------------------ 210s - f 210s -(1 row) 210s - 210s +ERROR: function is_valid_smiles(unknown) does not exist 210s +LINE 1: SELECT is_valid_smiles('c1cccn1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT is_valid_smarts('c1ccc[n,c]1'); 210s - is_valid_smarts 210s ------------------ 210s - t 210s -(1 row) 210s - 210s -SELECT mol_from_smarts('c1ccc[n,c]1'); 210s - mol_from_smarts 210s ------------------ 210s - *1cccc1 210s -(1 row) 210s - 210s +ERROR: function is_valid_smarts(unknown) does not exist 210s +LINE 1: SELECT is_valid_smarts('c1ccc[n,c]1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +SELECT qmol_from_smarts('c1ccc[n,c]1'); 210s +ERROR: function qmol_from_smarts(unknown) does not exist 210s +LINE 1: SELECT qmol_from_smarts('c1ccc[n,c]1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT is_valid_smarts('c1ccc'); 210s - is_valid_smarts 210s ------------------ 210s - f 210s -(1 row) 210s - 210s -SELECT mol_from_smarts('c1ccc'); 210s -WARNING: could not create molecule from SMILES 'c1ccc' 210s - mol_from_smarts 210s ------------------ 210s - 210s -(1 row) 210s - 210s +ERROR: function is_valid_smarts(unknown) does not exist 210s +LINE 1: SELECT is_valid_smarts('c1ccc'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +SELECT qmol_from_smarts('c1ccc'); 210s +ERROR: function qmol_from_smarts(unknown) does not exist 210s +LINE 1: SELECT qmol_from_smarts('c1ccc'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_to_smiles(mol_from_smiles('c1ccccc1')); 210s - mol_to_smiles 210s ---------------- 210s - c1ccccc1 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_to_smiles(mol_from_smiles('c1ccccc1')); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_to_smarts(mol_from_smiles('c1ccccc1')); 210s - mol_to_smarts 210s ----------------------------------- 210s - [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_to_smarts(mol_from_smiles('c1ccccc1')); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_to_smarts('c1cccc[n,c]1'::qmol); 210s - mol_to_smarts 210s ---------------- 210s - c1cccc[n,c]1 210s -(1 row) 210s - 210s +ERROR: type "qmol" does not exist 210s +LINE 1: SELECT mol_to_smarts('c1cccc[n,c]1'::qmol); 210s + ^ 210s SELECT mol_to_smiles('c1cccc[n,c]1'::qmol); 210s - mol_to_smiles 210s ---------------- 210s - *1ccccc1 210s -(1 row) 210s - 210s +ERROR: type "qmol" does not exist 210s +LINE 1: SELECT mol_to_smiles('c1cccc[n,c]1'::qmol); 210s + ^ 210s SELECT is_valid_smiles(''); 210s - is_valid_smiles 210s ------------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: function is_valid_smiles(unknown) does not exist 210s +LINE 1: SELECT is_valid_smiles(''); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_from_smiles(''); 210s - mol_from_smiles 210s ------------------ 210s - 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_from_smiles(''); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_to_smiles(mol_from_smiles('')); 210s - mol_to_smiles 210s ---------------- 210s - 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_to_smiles(mol_from_smiles('')); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s CREATE TABLE pgmol (id int, m mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: CREATE TABLE pgmol (id int, m mol); 210s + ^ 210s \copy pgmol from 'data/data' 210s +ERROR: relation "pgmol" does not exist 210s CREATE UNIQUE INDEX mol_ididx ON pgmol (id); 210s +ERROR: relation "pgmol" does not exist 210s SELECT count(*) FROM pgmol; 210s - count 210s -------- 210s - 1000 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s -SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccccc1'); 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s -SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1cccnc1'); 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s -SELECT count(*) FROM pgmol WHERE m @> mol_from_smarts('c1ccc[n,c]c1'); 210s - count 210s -------- 210s - 939 210s -(1 row) 210s - 210s -SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccccc1') <@ m; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s -SELECT count(*) FROM pgmol WHERE mol_from_smarts('c1ccc[n,c]c1') <@ m; 210s - count 210s -------- 210s - 939 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; 210s + ^ 210s +SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1ccccc1'); 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1cc... 210s + ^ 210s +SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1cccnc1'); 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1cc... 210s + ^ 210s +SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1ccc[n,c]c1'); 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> qmol_from_smarts('c1cc... 210s + ^ 210s +SELECT count(*) FROM pgmol WHERE qmol_from_smarts('c1ccccc1') <@ m; 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE qmol_from_smarts('c1ccccc1'... 210s + ^ 210s +SELECT count(*) FROM pgmol WHERE qmol_from_smarts('c1ccc[n,c]c1') <@ m; 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE qmol_from_smarts('c1ccc[n,c... 210s + ^ 210s SELECT id, rdkit_fp(m) AS f, maccs_fp(m) as maccsf INTO pgbfp FROM pgmol; 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: ...kit_fp(m) AS f, maccs_fp(m) as maccsf INTO pgbfp FROM pgmol; 210s + ^ 210s CREATE UNIQUE INDEX bfp_ididx ON pgbfp (id); 210s +ERROR: relation "pgbfp" does not exist 210s SELECT id, morgan_fp(m,1) AS f INTO pgsfp FROM pgmol; 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT id, morgan_fp(m,1) AS f INTO pgsfp FROM pgmol; 210s + ^ 210s CREATE UNIQUE INDEX sfp_ididx ON pgsfp (id); 210s +ERROR: relation "pgsfp" does not exist 210s SELECT id, torsion_fp(m) AS f INTO pgtorsfp FROM pgmol; 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT id, torsion_fp(m) AS f INTO pgtorsfp FROM pgmol; 210s + ^ 210s SELECT id, atompair_fp(m) AS f INTO pgpairfp FROM pgmol; 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT id, atompair_fp(m) AS f INTO pgpairfp FROM pgmol; 210s + ^ 210s set rdkit.tanimoto_threshold=0.5; 210s set rdkit.dice_threshold=0.5; 210s SELECT 210s @@ -188,10 +167,9 @@ 210s (SELECT * FROM pgbfp ORDER BY id) AS t 210s WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) % f 210s LIMIT 10; 210s - id | tanimoto_sml 210s -----+-------------- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 5: (SELECT * FROM pgbfp ORDER BY id) AS t 210s + ^ 210s SELECT 210s id, 210s dice_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f) 210s @@ -199,10 +177,9 @@ 210s (SELECT * FROM pgbfp ORDER BY id) AS t 210s WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) % f 210s LIMIT 10; 210s - id | dice_sml 210s -----+---------- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 5: (SELECT * FROM pgbfp ORDER BY id) AS t 210s + ^ 210s SELECT 210s id, 210s tanimoto_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f) 210s @@ -210,20 +187,9 @@ 210s (SELECT * FROM pgbfp ORDER BY id) AS t 210s WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) # f 210s LIMIT 10; 210s - id | tanimoto_sml 210s ---------+--------------------- 210s - 66722 | 0.3601036269430052 210s - 498250 | 0.3682983682983683 210s - 576770 | 0.35368421052631577 210s - 644427 | 0.3370165745856354 210s - 645921 | 0.36594202898550726 210s - 690546 | 0.402 210s - 698576 | 0.4226579520697168 210s - 714484 | 0.3830734966592428 210s - 771595 | 0.34393638170974156 210s - 788060 | 0.33386581469648563 210s -(10 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 5: (SELECT * FROM pgbfp ORDER BY id) AS t 210s + ^ 210s SELECT 210s id, 210s dice_sml(rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol), f), 210s @@ -232,20 +198,9 @@ 210s (SELECT * FROM pgbfp ORDER BY id) AS t 210s WHERE rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol) # f 210s LIMIT 10; 210s - id | dice_sml | size 210s ---------+--------------------+------ 210s - 66722 | 0.5295238095238095 | 1024 210s - 498250 | 0.5383304940374787 | 1024 210s - 576770 | 0.5225505443234837 | 1024 210s - 644427 | 0.5041322314049587 | 1024 210s - 645921 | 0.5358090185676393 | 1024 210s - 690546 | 0.5734664764621968 | 1024 210s - 698576 | 0.5941807044410413 | 1024 210s - 714484 | 0.5539452495974235 | 1024 210s - 771595 | 0.5118343195266272 | 1024 210s - 788060 | 0.5005988023952096 | 1024 210s -(10 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 6: (SELECT * FROM pgbfp ORDER BY id) AS t 210s + ^ 210s set rdkit.tanimoto_threshold=0.4; 210s SELECT 210s id, 210s @@ -254,11 +209,9 @@ 210s (SELECT * FROM pgsfp ORDER BY id) AS t 210s WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1) % f 210s LIMIT 10; 210s - id | tanimoto_sml 210s ----------+-------------------- 210s - 3761688 | 0.4418604651162791 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 5: (SELECT * FROM pgsfp ORDER BY id) AS t 210s + ^ 210s SELECT 210s id, 210s dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1), f) 210s @@ -266,11 +219,9 @@ 210s (SELECT * FROM pgsfp ORDER BY id) AS t 210s WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)))'::mol, 1) % f 210s LIMIT 10; 210s - id | dice_sml 210s ----------+-------------------- 210s - 3761688 | 0.6129032258064516 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 5: (SELECT * FROM pgsfp ORDER BY id) AS t 210s + ^ 210s SELECT 210s id, 210s tanimoto_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), f) 210s @@ -278,15 +229,9 @@ 210s (SELECT * FROM pgsfp ORDER BY id) AS t 210s WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1) # f 210s LIMIT 10; 210s - id | tanimoto_sml 210s -----------+--------------------- 210s - 902176 | 0.34782608695652173 210s - 2952787 | 0.36585365853658536 210s - 5281628 | 0.34615384615384615 210s - 10560368 | 0.4358974358974359 210s - 16196768 | 0.375 210s -(5 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 5: (SELECT * FROM pgsfp ORDER BY id) AS t 210s + ^ 210s SELECT 210s id, 210s dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), f) 210s @@ -294,93 +239,67 @@ 210s (SELECT * FROM pgsfp ORDER BY id) AS t 210s WHERE morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1) # f 210s LIMIT 10; 210s - id | dice_sml 210s -----------+-------------------- 210s - 902176 | 0.5161290322580645 210s - 2952787 | 0.5357142857142857 210s - 5281628 | 0.5142857142857142 210s - 10560368 | 0.6071428571428571 210s - 16196768 | 0.5454545454545454 210s -(5 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 5: (SELECT * FROM pgsfp ORDER BY id) AS t 210s + ^ 210s select dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; 210s - sml 210s --------------------- 210s - 0.8846153846153846 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...dice_sml(morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), m... 210s + ^ 210s select dice_sml(featmorgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), featmorgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; 210s - sml 210s --------------------- 210s - 0.8846153846153846 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ..._sml(featmorgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), f... 210s + ^ 210s select dice_sml(morganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), morganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; 210s - sml 210s --------------------- 210s - 0.8888888888888888 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ce_sml(morganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), m... 210s + ^ 210s select dice_sml(featmorganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), featmorganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)N)'::mol, 1)) sml; 210s - sml 210s --------------------- 210s - 0.9032258064516129 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ml(featmorganbv_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)'::mol, 1), f... 210s + ^ 210s select 'Cc1ccccc1'::mol@='c1ccccc1C'::mol; 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'Cc1ccccc1'::mol@='c1ccccc1C'::mol; 210s + ^ 210s select 'Cc1ccccc1'::mol@='c1ccccc1CC'::mol; 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'Cc1ccccc1'::mol@='c1ccccc1CC'::mol; 210s + ^ 210s select 'Cc1ccccc1'::mol@='c1cccnc1C'::mol; 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'Cc1ccccc1'::mol@='c1cccnc1C'::mol; 210s + ^ 210s select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1')); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: function torsion_fp(unknown) does not exist 210s +LINE 1: select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCN... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('NCC1CCOCC1')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function torsion_fp(unknown) does not exist 210s +LINE 1: select subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCN... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=add(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function torsion_fp(unknown) does not exist 210s +LINE 1: select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1')... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=add(torsion_fp('CCC1CCOCC1'),torsion_fp('NCC1CCOCC1')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function torsion_fp(unknown) does not exist 210s +LINE 1: select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1')... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function torsion_fp(unknown) does not exist 210s +LINE 1: select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1')... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1'))=subtract(torsion_fp('CCC1CCOCC1'),torsion_fp('OCC1CCOCC1')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function torsion_fp(unknown) does not exist 210s +LINE 1: select add(torsion_fp('CCC1CCNCC1'),torsion_fp('OCC1CCNCC1')... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select is_valid_ctab('chiral1.mol 210s ChemDraw04200416412D 210s 210s @@ -395,17 +314,15 @@ 210s 1 4 1 1 210s 1 5 1 0 210s M END'); 210s - is_valid_ctab 210s ---------------- 210s - t 210s -(1 row) 210s - 210s +ERROR: function is_valid_ctab(unknown) does not exist 210s +LINE 1: select is_valid_ctab('chiral1.mol 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select is_valid_ctab('invalid'); 210s - is_valid_ctab 210s ---------------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function is_valid_ctab(unknown) does not exist 210s +LINE 1: select is_valid_ctab('invalid'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select mol_from_ctab('chiral1.mol 210s ChemDraw04200416412D 210s 210s @@ -420,45 +337,22 @@ 210s 1 4 1 1 210s 1 5 1 0 210s M END'); 210s - mol_from_ctab 210s ----------------- 210s - C[C@](F)(Cl)Br 210s -(1 row) 210s - 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_from_ctab('chiral1.mol 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s -- mol_to_ctab() - suppress auto-generation of depiction. 210s select mol_to_ctab(mol('CCC'), false); 210s - mol_to_ctab 210s ------------------------------------------------------------------------ 210s - + 210s - RDKit 2D + 210s - + 210s - 3 2 0 0 0 0 0 0 0 0999 V2000 + 210s - 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1 2 1 0 + 210s - 2 3 1 0 + 210s - M END + 210s - 210s -(1 row) 210s - 210s +ERROR: function mol(unknown) does not exist 210s +LINE 1: select mol_to_ctab(mol('CCC'), false); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s -- mol_to_ctab() - with auto-generated depiction. 210s select mol_to_ctab(mol('CCC')); 210s - mol_to_ctab 210s ------------------------------------------------------------------------ 210s - + 210s - RDKit 2D + 210s - + 210s - 3 2 0 0 0 0 0 0 0 0999 V2000 + 210s - 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1 2 1 0 + 210s - 2 3 1 0 + 210s - M END + 210s - 210s -(1 row) 210s - 210s +ERROR: function mol(unknown) does not exist 210s +LINE 1: select mol_to_ctab(mol('CCC')); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s -- mol_to_ctab() - should preserve existing/input depiction. Note the 210s -- extra 'true' parameter to 'mol_from_ctab()' that forces the cartridge 210s -- to preserve the input conformer. Otherwise the conformer will be lost. 210s @@ -476,164 +370,348 @@ 210s 1 4 1 1 210s 1 5 1 0 210s M END', true)); 210s - mol_to_ctab 210s ------------------------------------------------------------------------ 210s - + 210s - RDKit 2D + 210s - + 210s - 5 4 0 0 0 0 0 0 0 0999 V2000 + 210s - -0.0141 0.0553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 0.8109 0.0553 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.4266 0.7697 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.0141 -0.7697 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.8109 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1 2 1 0 + 210s - 1 3 1 0 + 210s - 1 4 1 0 + 210s - 1 5 1 6 + 210s - M END + 210s - 210s -(1 row) 210s - 210s +ERROR: function mol_from_ctab(unknown, boolean) does not exist 210s +LINE 1: select mol_to_ctab(mol_from_ctab('chiral1.mol 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- mol_to_ctab() - force v3000. 210s +select mol_to_ctab(mol('CCC'), false, true); 210s +ERROR: function mol(unknown) does not exist 210s +LINE 1: select mol_to_ctab(mol('CCC'), false, true); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_to_v3kctab(mol('CCC'), false); 210s +ERROR: function mol(unknown) does not exist 210s +LINE 1: select mol_to_v3kctab(mol('CCC'), false); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select all_values_lt(torsion_fp('c1ccccc1C'::mol),2); 210s - all_values_lt 210s ---------------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select all_values_lt(torsion_fp('c1ccccc1C'::mol),2); 210s + ^ 210s select all_values_lt(torsion_fp('c1ccccc1C'::mol),3); 210s - all_values_lt 210s ---------------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select all_values_lt(torsion_fp('c1ccccc1C'::mol),3); 210s + ^ 210s select all_values_gt(torsion_fp('c1ccccc1C'::mol),1); 210s - all_values_gt 210s ---------------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select all_values_gt(torsion_fp('c1ccccc1C'::mol),1); 210s + ^ 210s select all_values_gt(torsion_fp('c1ccccc1C'::mol),2); 210s - all_values_gt 210s ---------------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select all_values_gt(torsion_fp('c1ccccc1C'::mol),2); 210s + ^ 210s select is_valid_mol_pkl('foo'::bytea); 210s - is_valid_mol_pkl 210s ------------------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function is_valid_mol_pkl(bytea) does not exist 210s +LINE 1: select is_valid_mol_pkl('foo'::bytea); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select is_valid_mol_pkl(mol_to_pkl('c1ccccc1'::mol)); 210s - is_valid_mol_pkl 210s ------------------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select is_valid_mol_pkl(mol_to_pkl('c1ccccc1'::mol)); 210s + ^ 210s select mol_from_pkl(mol_to_pkl('c1ccccc1'::mol)); 210s - mol_from_pkl 210s --------------- 210s - c1ccccc1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_from_pkl(mol_to_pkl('c1ccccc1'::mol)); 210s + ^ 210s select tanimoto_sml(morganbv_fp('c1ccccn1'::mol),morganbv_fp('c1ccccc1'::mol)); 210s - tanimoto_sml 210s --------------------- 210s - 0.3333333333333333 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select tanimoto_sml(morganbv_fp('c1ccccn1'::mol),morganbv_fp... 210s + ^ 210s select tanimoto_sml(bfp_from_binary_text(bfp_to_binary_text(morganbv_fp('c1ccccn1'::mol))), 210s bfp_from_binary_text(bfp_to_binary_text(morganbv_fp('c1ccccc1'::mol)))); 210s - tanimoto_sml 210s --------------------- 210s - 0.3333333333333333 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...nary_text(bfp_to_binary_text(morganbv_fp('c1ccccn1'::mol))), 210s + ^ 210s -- GitHub issue 9 210s select 'C1CC2CC3C45C2C2C6C7C8C9C%10C(C1)C1C%11%10C%109C98C87C76C42C24C65C3C3C56C64C4%12C72C28C79C8%10C9%11C1C1C%109C98C87C42C24C7%12C%116C65C3C3C56C6%11C%117C74C4%12C82C29C8%10C1C1C98C42C24C89C1C1C98C84C4%10C%122C27C7%11C%116C65C3C3C56C6%11C%117C42C24C7%11C%116C65C3C3C56C6%11C%117C74C4%12C%102C28C89C1C1C98C42C24C89C1C1C98C84C4%10C%122C27C7%11C%116C65C3C3C56C6%11C%117C42C24C7%11C%116C65C3C3C56C6%11C%117C74C4%12C%102C28C89C1C1C98C42C24C89C1CC8C4C1C%122C27C4%11C76C65C3CC6C7C4C12'::mol; 210s - mol 210s ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - C1CC2CC3C4C5C6C7C8C9C%10C%11C%12C%13C%14C%15C%16CC%17C%18C%19C%20C%21C%22C%23CC%24C%25C%26C%27C%28C%29C%30C%31C%32C%33C%34C%35C%36C%37C(C1)C1C%38C%39C%40C%41C%42C2C32C%423C%41%42C%40%41C%39%40C%38%39C1%37C%361C%35%36C%34%35C%33%34C%32%33C%31%32C%30%31C%29%30C%28%29C%27%28C%26%27C%25%26C%23%24C%22%23C%21%22C%20%21C%19%20C%18%19C%17%16C%15%16C%14%15C%13%14C%12%13C%11%12C%10%11C9%10C89C78C67C56C42C32C%423C%414C%405C%391C%361C%35%17C%34%18C%33%24C%32%25C%31%32C%30%31C%29%30C%28%29C%27%28C%23%26C%22%23C%21%22C%20%21C%19%16C%15%16C%14%15C%13%14C%12%13C%11%12C%10%11C9%10C89C78C62C32C43C51C%171C%184C%245C%256C%327C%31%17C%30%18C%29%19C%23%28C%22%20C%21%16C%15%16C%14%15C%13%14C%12%13C%11%12C%10%11C9%10C82C31C%104C%115C%126C%137C%14%17C%15%18C%20%16%19 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...1C98C42C24C89C1CC8C4C1C%122C27C4%11C76C65C3CC6C7C4C12'::mol; 210s + ^ 210s -- chiral matching 210s +set rdkit.do_chiral_sss=false; 210s select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match; 210s + ^ 210s select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match; 210s + ^ 210s select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match; 210s + ^ 210s set rdkit.do_chiral_sss=true; 210s select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@>'CC(F)Cl'::mol as match; 210s + ^ 210s select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@>'C[C@H](F)Cl'::mol as match; 210s + ^ 210s select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match; 210s - match 210s -------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@>'C[C@@H](F)Cl'::mol as match; 210s + ^ 210s +set rdkit.do_chiral_sss=false; 210s +-- github #2790 210s set rdkit.do_chiral_sss=false; 210s +select 'C[C@H](F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s + ^ 210s +select 'C[C@H](F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s + ^ 210s +select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol; 210s + ^ 210s +select 'CC(F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC(F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s + ^ 210s +select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s + ^ 210s +select 'CC(F)Cl'::mol@='CC(F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC(F)Cl'::mol@='CC(F)Cl'::mol; 210s + ^ 210s +set rdkit.do_chiral_sss=true; 210s +select 'C[C@H](F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s + ^ 210s +select 'C[C@H](F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s + ^ 210s +select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](F)Cl'::mol@='CC(F)Cl'::mol; 210s + ^ 210s +select 'CC(F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC(F)Cl'::mol@='C[C@@H](F)Cl'::mol; 210s + ^ 210s +select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC(F)Cl'::mol@='C[C@H](F)Cl'::mol; 210s + ^ 210s +select 'CC(F)Cl'::mol@='CC(F)Cl'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC(F)Cl'::mol@='CC(F)Cl'::mol; 210s + ^ 210s +set rdkit.do_chiral_sss=false; 210s +-- Enhanced stereo 210s +set rdkit.do_chiral_sss=false; 210s +set rdkit.do_enhanced_stereo_sss=false; /* has no effect when do_chiral_sss is false */ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 2: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +set rdkit.do_enhanced_stereo_sss=true; /* has no effect when do_chiral_sss is false */ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 2: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +set rdkit.do_chiral_sss=true; 210s +set rdkit.do_enhanced_stereo_sss=false; 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +set rdkit.do_enhanced_stereo_sss=true; /* now we expect to see an effect */ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 2: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@H](O)[C@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C@@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@@H](O)[C... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@H](C)F'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol@>'C[C@H](O)[C@... 210s + ^ 210s +set rdkit.do_chiral_sss=false; 210s +set rdkit.do_enhanced_stereo_sss=false; 210s +-- forcing chiral queries 210s +select substruct_chiral('C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...bstruct_chiral('C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol,'C[C@@... 210s + ^ 210s +select substruct_chiral('C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...bstruct_chiral('C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol,'C[C@@... 210s + ^ 210s +select rsubstruct_chiral('C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...bstruct_chiral('C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol,'C[C@@... 210s + ^ 210s +select rsubstruct_chiral('C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol,'C[C@@H](O)[C@@H](C)F |&1:1,3,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...bstruct_chiral('C[C@@H](O)[C@@H](C)F |o1:1,3,r|'::mol,'C[C@@... 210s + ^ 210s -- substructure counts 210s select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol); 210s - substruct_count 210s ------------------ 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol); 210s + ^ 210s select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol,false); 210s - substruct_count 210s ------------------ 210s - 2 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct_count('c1ccncc1'::mol,'c1ccncc1'::mol,false... 210s + ^ 210s +select substruct_count('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ..._count('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccc... 210s + ^ 210s +select substruct_count('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ..._count('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccc... 210s + ^ 210s +select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccc... 210s + ^ 210s +select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccc... 210s + ^ 210s +select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,false); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,'c1ccc... 210s + ^ 210s +select substruct_count_chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccccc1C[C@@H](O)[C@@H](C)F |&1:7,9,r|'::mol,false); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...chiral('c1ccccc1C[C@@H](O)[C@@H](C)F |o1:7,9,r|'::mol,'c1ccc... 210s + ^ 210s -- special queries 210s select 'c1ccc[nH]1'::mol@>mol_from_smiles('c1cccn1[H]') as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1ccc[nH]1'::mol@>mol_from_smiles('c1cccn1[H]') as m... 210s + ^ 210s select 'c1cccn1C'::mol@>mol_from_smiles('c1cccn1[H]') as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccn1C'::mol@>mol_from_smiles('c1cccn1[H]') as mat... 210s + ^ 210s select 'c1ccc[nH]1'::mol@>qmol_from_smiles('c1cccn1[H]') as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1ccc[nH]1'::mol@>qmol_from_smiles('c1cccn1[H]') as ... 210s + ^ 210s select 'c1cccn1C'::mol@>qmol_from_smiles('c1cccn1[H]') as match; 210s - match 210s -------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccn1C'::mol@>qmol_from_smiles('c1cccn1[H]') as ma... 210s + ^ 210s select 'c1ccc[nH]1'::mol@>mol_from_ctab('query 210s Mrv0541 04021509592D 210s 210s @@ -651,11 +729,9 @@ 210s 3 4 1 0 0 0 0 210s 1 6 1 0 0 0 0 210s M END') as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1ccc[nH]1'::mol@>mol_from_ctab('query 210s + ^ 210s select 'c1cccn1C'::mol@>mol_from_ctab('query 210s Mrv0541 04021509592D 210s 210s @@ -673,11 +749,9 @@ 210s 3 4 1 0 0 0 0 210s 1 6 1 0 0 0 0 210s M END') as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccn1C'::mol@>mol_from_ctab('query 210s + ^ 210s select 'c1ccc[nH]1'::mol@>qmol_from_ctab('query 210s Mrv0541 04021509592D 210s 210s @@ -695,11 +769,9 @@ 210s 3 4 1 0 0 0 0 210s 1 6 1 0 0 0 0 210s M END') as match; 210s - match 210s -------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1ccc[nH]1'::mol@>qmol_from_ctab('query 210s + ^ 210s select 'c1cccn1C'::mol@>qmol_from_ctab('query 210s Mrv0541 04021509592D 210s 210s @@ -717,162 +789,358 @@ 210s 3 4 1 0 0 0 0 210s 1 6 1 0 0 0 0 210s M END') as match; 210s - match 210s -------- 210s - f 210s -(1 row) 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccn1C'::mol@>qmol_from_ctab('query 210s + ^ 210s +-- github #4787: 210s +select mol_to_smarts(qmol_from_ctab('query 210s + Mrv0541 04021509592D 210s + 210s + 6 6 0 0 0 0 999 V2000 210s + -0.2652 0.7248 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 210s + -0.9796 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + -0.9796 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.4493 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.4493 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + -0.2652 -0.1002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1 2 1 0 0 0 0 210s + 2 3 2 0 0 0 0 210s + 4 5 2 0 0 0 0 210s + 1 5 1 0 0 0 0 210s + 3 4 1 0 0 0 0 210s + 1 6 1 0 0 0 0 210s +M END')); 210s +ERROR: function qmol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_to_smarts(qmol_from_ctab('query 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_to_smarts(qmol_from_ctab('query 210s + Mrv0541 04021509592D 210s 210s + 6 6 0 0 0 0 999 V2000 210s + -0.2652 0.7248 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 210s + -0.9796 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + -0.9796 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.4493 1.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.4493 1.1373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 210s + -0.2652 -0.1002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1 2 4 0 0 0 0 210s + 2 3 4 0 0 0 0 210s + 4 5 4 0 0 0 0 210s + 1 5 4 0 0 0 0 210s + 3 4 4 0 0 0 0 210s + 1 6 1 0 0 0 0 210s +M END')); 210s +ERROR: function qmol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_to_smarts(qmol_from_ctab('query 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_to_smarts(qmol_from_ctab('Boronate acid/ester(aryl) 210s + SciTegic12012112112D 210s + 210s + 5 4 0 0 0 0 999 V2000 210s + 1.7243 -2.7324 0.0000 A 0 0 210s + 2.7559 -2.1456 0.0000 C 0 0 210s + 3.7808 -2.7324 0.0000 B 0 0 210s + 4.8057 -2.1456 0.0000 O 0 0 210s + 3.7808 -3.9190 0.0000 O 0 0 210s + 1 2 4 0 0 1 0 210s + 2 3 1 0 210s + 3 4 1 0 210s + 3 5 1 0 210s +M END')); 210s +ERROR: function qmol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_to_smarts(qmol_from_ctab('Boronate acid/ester(ary... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_to_smarts(qmol_from_smiles('c:c')); 210s +ERROR: function qmol_from_smiles(unknown) does not exist 210s +LINE 1: select mol_to_smarts(qmol_from_smiles('c:c')); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_to_smarts(qmol_from_smiles('C1=CC=CC=C1')); 210s +ERROR: function qmol_from_smiles(unknown) does not exist 210s +LINE 1: select mol_to_smarts(qmol_from_smiles('C1=CC=CC=C1')); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s -- mol_adjust_query_properties 210s select 'C1CC1OC'::mol @> 'C1CC1O*'::mol; 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1OC'::mol @> 'C1CC1O*'::mol; 210s + ^ 210s select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O... 210s + ^ 210s select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol,'{"makeDummiesQueries":false}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O... 210s + ^ 210s select 'CC1CC1OC'::mol @> 'C1CC1O*'::mol; 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC1CC1OC'::mol @> 'C1CC1O*'::mol; 210s + ^ 210s select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1... 210s + ^ 210s select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1O*'::mol,'{"adjustDegree":false}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CC1CC1OC'::mol @> mol_adjust_query_properties('C1CC1... 210s + ^ 210s select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1CC1CO*'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1... 210s + ^ 210s select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1CC1CO*'::mol,'{"adjustDegreeFlags":"IGNOREDUMMIES"}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1C(C)OC'::mol @> mol_adjust_query_properties('C1... 210s + ^ 210s select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC... 210s + ^ 210s select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORENONE"}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC... 210s + ^ 210s select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNOREALL"}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC... 210s + ^ 210s select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORECHAINS"}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC... 210s + ^ 210s select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS"}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC... 210s + ^ 210s select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS|IGNORECHAINS"}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1CC1CCCC'::mol @> mol_adjust_query_properties('C1CC... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORENONE"}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNOREALL"}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORECHAINS"}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS"}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"IGNORERINGS|IGNORECHAINS"}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"bogus"}'); 210s -ERROR: bad which string provided 'BOGUS' 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C... 210s + ^ 210s select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties... 210s + ^ 210s select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegree":false}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties... 210s + ^ 210s select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegree":false,"adjustHeavyDegree":true}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'C1C([2H])C1CCCC'::mol @> mol_adjust_query_properties... 210s + ^ 210s +select mol_to_smarts(mol_adjust_query_properties('*c1ncc(*)cc1'::mol)); 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...to_smarts(mol_adjust_query_properties('*c1ncc(*)cc1'::mol)); 210s + ^ 210s +select mol_to_smarts(mol_adjust_query_properties('*c1ncc(*)cc1'::qmol)); 210s +ERROR: type "qmol" does not exist 210s +LINE 1: ...o_smarts(mol_adjust_query_properties('*c1ncc(*)cc1'::qmol)); 210s + ^ 210s -- CXSmiles 210s -SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5|')); 210s - mol_to_smiles 210s ------------------------------- 210s - C[C@H](F)[C@H](C)[C@@H](C)Br 210s -(1 row) 210s - 210s -SELECT mol_to_cxsmiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5|')); 210s - mol_to_cxsmiles 210s -------------------------------------------- 210s - C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:4,5| 210s -(1 row) 210s - 210s +SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|')); 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_to_smiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +SELECT mol_to_cxsmiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|')); 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_to_cxsmiles(mol_from_smiles('C[C@H](F)[C@H](C)[C@... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +SELECT mol_to_cxsmarts(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|')); 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_to_cxsmarts(mol_from_smiles('C[C@H](F)[C@H](C)[C@... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +SELECT mol_to_cxsmarts(qmol_from_smarts('C[C@H]([F,Cl,Br])[C@H](C)[C@@H](C)Br |a:1,o1:3,5|')); 210s +ERROR: function qmol_from_smarts(unknown) does not exist 210s +LINE 1: SELECT mol_to_cxsmarts(qmol_from_smarts('C[C@H]([F,Cl,Br])[C... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- CXSmiles from mol_out 210s +SELECT mol_out(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br |a:1,o1:3,5|')); 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_out(mol_from_smiles('C[C@H](F)[C@H](C)[C@@H](C)Br... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- github #3688: bad input to qmol_from_ctab() crashes db 210s +select qmol_from_ctab('a'::cstring,false); 210s +ERROR: function qmol_from_ctab(cstring, boolean) does not exist 210s +LINE 1: select qmol_from_ctab('a'::cstring,false); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- github #3689: bad input to qmol_from_smiles() crashes db 210s +select qmol_from_smiles('a'::cstring); 210s +ERROR: function qmol_from_smiles(cstring) does not exist 210s +LINE 1: select qmol_from_smiles('a'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select qmol_from_smiles('C1C'::cstring); 210s +ERROR: function qmol_from_smiles(cstring) does not exist 210s +LINE 1: select qmol_from_smiles('C1C'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- casting from mol to qmol 210s +select mol_from_smiles('C=C')::qmol; 210s +ERROR: type "qmol" does not exist 210s +LINE 1: select mol_from_smiles('C=C')::qmol; 210s + ^ 210s +-- github #5095: cannot restore molecule 210s +select mol_in('c1cccc'::cstring); 210s +ERROR: function mol_in(cstring) does not exist 210s +LINE 1: select mol_in('c1cccc'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_in('c1cccc1'::cstring); 210s +ERROR: function mol_in(cstring) does not exist 210s +LINE 1: select mol_in('c1cccc1'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_in('c1co(C)cc1'::cstring); 210s +ERROR: function mol_in(cstring) does not exist 210s +LINE 1: select mol_in('c1co(C)cc1'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_in('c1cccc'::cstring); 210s +ERROR: function mol_in(cstring) does not exist 210s +LINE 1: select mol_in('c1cccc'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select mol_in('CN(=O)=O'::cstring); 210s +ERROR: function mol_in(cstring) does not exist 210s +LINE 1: select mol_in('CN(=O)=O'::cstring); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select 'CN(=O)=O'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CN(=O)=O'::mol; 210s + ^ 210s +select 'c1cccc1'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccc1'::mol; 210s + ^ 210s +select 'c1co(C)cc1'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1co(C)cc1'::mol; 210s + ^ 210s +select mol_in('c1cccc1'::cstring) @> '[r5]'::qmol; 210s +ERROR: function mol_in(cstring) does not exist 210s +LINE 1: select mol_in('c1cccc1'::cstring) @> '[r5]'::qmol; 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select 'c1cccc1'::mol @> '[r5]'::qmol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccc1'::mol @> '[r5]'::qmol; 210s + ^ 210s +select mol_in('Cc1ccc2c(c1)-n1-c(=O)c=cc(=O)-n-2-c2cc(C)ccc2-1'); 210s +ERROR: function mol_in(unknown) does not exist 210s +LINE 1: select mol_in('Cc1ccc2c(c1)-n1-c(=O)c=cc(=O)-n-2-c2cc(C)ccc2... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +select 'c1cccc1'::text::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccc1'::text::mol; 210s + ^ 210s +select 'c1cccc1'::varchar::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1cccc1'::varchar::mol; 210s + ^ 210s +select mol_from_smiles('CCN(=O)=O') @> 'CN(=O)=O'; 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: select mol_from_smiles('CCN(=O)=O') @> 'CN(=O)=O'; 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- github #6002: molcmp failure 210s +select mol_cmp(mol_from_ctab(' 210s + Mrv2211 02092314292D 210s + 210s + 5 4 0 0 0 0 999 V2000 210s + 0.0000 3.6020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.7145 4.0145 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1.4290 4.4270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1.1270 3.3001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.3020 4.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1 2 6 0 0 0 0 210s + 2 3 2 0 0 0 0 210s + 2 4 2 0 0 0 0 210s + 2 5 6 0 0 0 0 210s +M END'),mol_from_ctab(' 210s + Mrv2211 02092314292D 210s + 210s + 5 4 0 0 0 0 999 V2000 210s + 0.0000 3.6020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.7145 4.0145 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1.4290 4.4270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1.1270 3.3001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 0.3020 4.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 210s + 1 2 6 0 0 0 0 210s + 2 3 2 0 0 0 0 210s + 2 4 2 0 0 0 0 210s + 2 5 6 0 0 0 0 210s +M END')); 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_cmp(mol_from_ctab(' 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s +-- mol properties being properly serialized 210s +select 'COC1=NNC=C1 |LN:1:1.3|'::mol; 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COC1=NNC=C1 |LN:1:1.3|'::mol; 210s + ^ 210s +-- bond properties all preserved 210s +select mol_to_v3kctab(mol_from_ctab(' 210s + Mrv2211 09062306242D 210s + 210s + 0 0 0 0 0 999 V3000 210s +M V30 BEGIN CTAB 210s +M V30 COUNTS 5 3 0 0 0 210s +M V30 BEGIN ATOM 210s +M V30 1 C -7.7917 4.0833 0 0 210s +M V30 2 C -6.458 4.8533 0 0 210s +M V30 3 C -5.1243 4.0833 0 0 210s +M V30 4 * -6.458 4.34 0 0 210s +M V30 5 C -5.303 6.3405 0 0 210s +M V30 END ATOM 210s +M V30 BEGIN BOND 210s +M V30 1 1 1 2 210s +M V30 2 2 2 3 210s +M V30 3 1 4 5 ENDPTS=(3 1 2 3) ATTACH=ANY 210s +M V30 END BOND 210s +M V30 END CTAB 210s +M END')); 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_to_v3kctab(mol_from_ctab(' 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/props.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/props.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/props.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/props.out 2024-11-23 20:44:12.134702166 +0000 210s @@ -1,341 +1,228 @@ 210s SET extra_float_digits=0; 210s SELECT mol_amw('c1ccccc1'::mol) mol_amw; 210s - mol_amw 210s ---------- 210s - 78.114 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_amw('c1ccccc1'::mol) mol_amw; 210s + ^ 210s SELECT mol_exactmw('c1ccccc1'::mol) mol_exactmw; 210s - mol_exactmw 210s -------------- 210s - 78.047 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_exactmw('c1ccccc1'::mol) mol_exactmw; 210s + ^ 210s SELECT mol_logp('c1ccccc1'::mol) mol_logp; 210s - mol_logp 210s ----------- 210s - 1.6866 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_logp('c1ccccc1'::mol) mol_logp; 210s + ^ 210s SELECT mol_hba('c1ccccc1'::mol) mol_hba; 210s - mol_hba 210s ---------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hba('c1ccccc1'::mol) mol_hba; 210s + ^ 210s SELECT mol_hbd('c1ccccc1'::mol) mol_hbd; 210s - mol_hbd 210s ---------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hbd('c1ccccc1'::mol) mol_hbd; 210s + ^ 210s SELECT mol_hba('c1ccncc1'::mol) mol_hba; 210s - mol_hba 210s ---------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hba('c1ccncc1'::mol) mol_hba; 210s + ^ 210s SELECT mol_hbd('c1ccncc1'::mol) mol_hbd; 210s - mol_hbd 210s ---------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hbd('c1ccncc1'::mol) mol_hbd; 210s + ^ 210s SELECT mol_hbd('c1ccncc1O'::mol) mol_hbd; 210s - mol_hbd 210s ---------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hbd('c1ccncc1O'::mol) mol_hbd; 210s + ^ 210s SELECT mol_hba('c1ccncc1O'::mol) mol_hba; 210s - mol_hba 210s ---------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hba('c1ccncc1O'::mol) mol_hba; 210s + ^ 210s SELECT mol_logp('c1ccncc1O'::mol) mol_logp; 210s - mol_logp 210s ----------- 210s - 0.7872 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_logp('c1ccncc1O'::mol) mol_logp; 210s + ^ 210s SELECT mol_chi0n('c1ccccc1O'::mol) v; 210s - v 210s ---------- 210s - 3.83396 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi0n('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi1n('c1ccccc1O'::mol) v; 210s - v 210s ---------- 210s - 2.13429 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi1n('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi2n('c1ccccc1O'::mol) v; 210s - v 210s ---------- 210s - 1.33555 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi2n('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi3n('c1ccccc1O'::mol) v; 210s - v 210s ----------- 210s - 0.756194 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi3n('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi4n('c1ccccc1O'::mol) v; 210s - v 210s ----------- 210s - 0.427994 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi4n('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi0v('c1ccccc1O'::mol) v; 210s - v 210s ---------- 210s - 3.83396 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi0v('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi1v('c1ccccc1O'::mol) v; 210s - v 210s ---------- 210s - 2.13429 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi1v('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi2v('c1ccccc1O'::mol) v; 210s - v 210s ---------- 210s - 1.33555 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi2v('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi3v('c1ccccc1O'::mol) v; 210s - v 210s ----------- 210s - 0.756194 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi3v('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_chi4v('c1ccccc1O'::mol) v; 210s - v 210s ----------- 210s - 0.427994 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_chi4v('c1ccccc1O'::mol) v; 210s + ^ 210s SELECT mol_kappa1('C12CC2C3CC13'::mol) v; 210s - v 210s ---------- 210s - 2.34375 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_kappa1('C12CC2C3CC13'::mol) v; 210s + ^ 210s SELECT mol_kappa2('CC(C)C1CCC(C)CCC1'::mol) v; 210s - v 210s ---------- 210s - 4.13265 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_kappa2('CC(C)C1CCC(C)CCC1'::mol) v; 210s + ^ 210s SELECT mol_kappa3('CC(C)C1CCC(C)CCC1'::mol) v; 210s - v 210s ---------- 210s - 2.84444 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_kappa3('CC(C)C1CCC(C)CCC1'::mol) v; 210s + ^ 210s SELECT mol_numspiroatoms('C1CCC2(C1)CC1CCC2CC1'::mol) v; 210s - v 210s ---- 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numspiroatoms('C1CCC2(C1)CC1CCC2CC1'::mol) v; 210s + ^ 210s SELECT mol_numbridgeheadatoms('C1CCC2(C1)CC1CCC2CC1'::mol) v; 210s - v 210s ---- 210s - 2 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ELECT mol_numbridgeheadatoms('C1CCC2(C1)CC1CCC2CC1'::mol) v; 210s + ^ 210s SELECT mol_numspiroatoms('CC1(C)CC2(C)CCC1(C)CC2'::mol) v; 210s - v 210s ---- 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numspiroatoms('CC1(C)CC2(C)CCC1(C)CC2'::mol) v; 210s + ^ 210s SELECT mol_numbridgeheadatoms('CC1(C)CC2(C)CCC1(C)CC2'::mol) v; 210s - v 210s ---- 210s - 2 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ECT mol_numbridgeheadatoms('CC1(C)CC2(C)CCC1(C)CC2'::mol) v; 210s + ^ 210s SELECT mol_phi('CC(C)(C)C(C)C'::mol) v; 210s - v 210s ---------- 210s - 1.85185 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_phi('CC(C)(C)C(C)C'::mol) v; 210s + ^ 210s SELECT mol_hallkieralpha('CC(O)(C)C(C)C'::mol) v; 210s - v 210s -------- 210s - -0.04 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_hallkieralpha('CC(O)(C)C(C)C'::mol) v; 210s + ^ 210s SELECT mol_numamidebonds('O=C(C)NC'::mol) v; 210s - v 210s ---- 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numamidebonds('O=C(C)NC'::mol) v; 210s + ^ 210s -- Mol formula tests - SQL equivalents of tests in testMolDescriptors.py. 210s select mol_formula('[2H]C([3H])O'::mol); 210s - mol_formula 210s -------------- 210s - CH4O 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_formula('[2H]C([3H])O'::mol); 210s + ^ 210s -- separateIsotopes = true 210s select mol_formula('[2H]C([3H])O'::mol, true); 210s - mol_formula 210s -------------- 210s - CH2DTO 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_formula('[2H]C([3H])O'::mol, true); 210s + ^ 210s -- abbreviateHIsotopes = false 210s select mol_formula('[2H]C([3H])O'::mol, true, false); 210s - mol_formula 210s --------------- 210s - CH2[2H][3H]O 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_formula('[2H]C([3H])O'::mol, true, false); 210s + ^ 210s -- 210s select mol_formula('[2H][13CH2]CO'::mol); 210s - mol_formula 210s -------------- 210s - C2H6O 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_formula('[2H][13CH2]CO'::mol); 210s + ^ 210s select mol_formula('[2H][13CH2]CO'::mol, true); 210s - mol_formula 210s -------------- 210s - C[13C]H5DO 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_formula('[2H][13CH2]CO'::mol, true); 210s + ^ 210s select mol_formula('[2H][13CH2]CO'::mol, true, false); 210s - mol_formula 210s ---------------- 210s - C[13C]H5[2H]O 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_formula('[2H][13CH2]CO'::mol, true, false); 210s + ^ 210s -- 210s SELECT mol_numrotatablebonds('CCC'::mol) mol_numrotatablebonds; 210s - mol_numrotatablebonds 210s ------------------------ 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numrotatablebonds('CCC'::mol) mol_numrotatablebon... 210s + ^ 210s SELECT mol_numrotatablebonds('CCCC'::mol) mol_numrotatablebonds; 210s - mol_numrotatablebonds 210s ------------------------ 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numrotatablebonds('CCCC'::mol) mol_numrotatablebo... 210s + ^ 210s -- mol_from_smiles() shouldn't be necessary, but there's an RDKit bug (#5104) 210s SELECT mol_numrotatablebonds(mol_from_smiles('c1ccccc1c1ccc(CCC)cc1')) mol_numrotatablebonds; 210s - mol_numrotatablebonds 210s ------------------------ 210s - 3 210s -(1 row) 210s - 210s +ERROR: function mol_from_smiles(unknown) does not exist 210s +LINE 1: SELECT mol_numrotatablebonds(mol_from_smiles('c1ccccc1c1ccc(... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT mol_numheavyatoms('CCC'::mol) val; 210s - val 210s ------ 210s - 3 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numheavyatoms('CCC'::mol) val; 210s + ^ 210s SELECT mol_numatoms('CCC'::mol) val; 210s - val 210s ------ 210s - 11 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numatoms('CCC'::mol) val; 210s + ^ 210s SELECT mol_numheteroatoms('CCC'::mol) val; 210s - val 210s ------ 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numheteroatoms('CCC'::mol) val; 210s + ^ 210s SELECT mol_numheteroatoms('CCO'::mol) val; 210s - val 210s ------ 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numheteroatoms('CCO'::mol) val; 210s + ^ 210s SELECT mol_tpsa('CCC'::mol) val; 210s - val 210s ------ 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_tpsa('CCC'::mol) val; 210s + ^ 210s SELECT mol_tpsa('CCO'::mol) val; 210s - val 210s -------- 210s - 20.23 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_tpsa('CCO'::mol) val; 210s + ^ 210s SELECT mol_labuteasa('CCC'::mol) val; 210s - val 210s ---------- 210s - 21.4691 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_labuteasa('CCC'::mol) val; 210s + ^ 210s SELECT mol_numrings('CCC'::mol) val; 210s - val 210s ------ 210s - 0 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numrings('CCC'::mol) val; 210s + ^ 210s SELECT mol_numrings('C1CC1'::mol) val; 210s - val 210s ------ 210s - 1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_numrings('C1CC1'::mol) val; 210s + ^ 210s SELECT mol_murckoscaffold('c1ccccc1CCC'::mol) val; 210s - val 210s ----------- 210s - c1ccccc1 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_murckoscaffold('c1ccccc1CCC'::mol) val; 210s + ^ 210s SELECT mol_murckoscaffold('CSC(C)=O'::mol) is NULL; 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT mol_murckoscaffold('CSC(C)=O'::mol) is NULL; 210s + ^ 210s SELECT substring(mol_to_svg('CCO'::mol)::text,1,120) svg; 210s - svg 210s ---------------------------------------------- 210s - + 210s - + 210s - + 210s - = 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 742 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 210s m > 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 742 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s SELECT * FROM pgmol WHERE 210s m = 'Clc1nccnc1NN=Cc1ccc(Br)cc1'; 210s - id | m 210s ----------+---------------------------- 210s - 2842150 | Clc1nccnc1NN=Cc1ccc(Br)cc1 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT * FROM pgmol WHERE 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 210s m < 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 258 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 210s m <= 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 258 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 210s m = 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 210s m >= 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 742 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 210s m > 'C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'; 210s - count 210s -------- 210s - 742 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX molidx; 210s +ERROR: index "molidx" does not exist 210s CREATE INDEX fpidx ON pgbfp (f); 210s +ERROR: relation "pgbfp" does not exist 210s SET enable_indexscan=off; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s SELECT * FROM pgbfp WHERE 210s f = rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - id | f | maccsf 210s -----+---+-------- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT * FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f < rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 31 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f <= rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 31 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f = rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f >= rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 969 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f > rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 969 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s SELECT * FROM pgbfp WHERE 210s f = rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - id | f | maccsf 210s -----+---+-------- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT * FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f < rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 31 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f <= rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 31 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f = rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f >= rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 969 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SELECT count(*) FROM pgbfp WHERE 210s f > rdkit_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol); 210s - count 210s -------- 210s - 969 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgbfp WHERE 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX fpidx; 210s +ERROR: index "fpidx" does not exist 210s CREATE INDEX fpidx ON pgsfp (f); 210s +ERROR: relation "pgsfp" does not exist 210s SET enable_indexscan=off; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s SELECT * FROM pgsfp WHERE 210s f = morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - id | f 210s -----+--- 210s -(0 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT * FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f < morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 55 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f <= morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 55 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f = morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f >= morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 945 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f > morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 945 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s SELECT * FROM pgsfp WHERE 210s f = morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - id | f 210s -----+--- 210s -(0 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT * FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f < morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 55 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f <= morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 55 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f = morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 0 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f >= morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 945 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SELECT count(*) FROM pgsfp WHERE 210s f > morgan_fp('C1C(OC2=CC(=CC(=C2C1=O)O)O)C3=CC(=C(C=C3)O)O'::mol, 1); 210s - count 210s -------- 210s - 945 210s -(1 row) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 1: SELECT count(*) FROM pgsfp WHERE 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX fpidx; 210s +ERROR: index "fpidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/molgist.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/molgist.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/molgist.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/molgist.out 2024-11-23 20:44:12.192679339 +0000 210s @@ -1,216 +1,177 @@ 210s CREATE INDEX molidx ON pgmol USING gist (m); 210s +ERROR: relation "pgmol" does not exist 210s SET rdkit.tanimoto_threshold = 0.8; 210s SET rdkit.dice_threshold = 0.8; 210s SET enable_indexscan=off; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1C(=O)N'; 210s - count 210s -------- 210s - 141 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1C(=O)N'; 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1cccnc1'; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; 210s - count 210s -------- 210s - 901 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 'c1ccccc1' <@ m; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; 210s - count 210s -------- 210s - 245 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE 'c1cccnc1' <@ m; 210s + ^ 210s SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1C(=O)N'; 210s - count 210s -------- 210s - 141 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgmol WHERE m @> 'c1ccccc1C(=O)N'; 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX molidx; 210s +ERROR: index "molidx" does not exist 210s -- ############################### 210s -- github issue #525 210s CREATE TABLE chemblmol (molregno int, m mol); 210s +ERROR: type "mol" does not exist 210s +LINE 1: CREATE TABLE chemblmol (molregno int, m mol); 210s + ^ 210s \copy chemblmol from 'data/chembl20_100.csv' (format csv) 210s +ERROR: relation "chemblmol" does not exist 210s CREATE INDEX mol_idx2 ON chemblmol using gist(m); 210s +ERROR: relation "chemblmol" does not exist 210s select * into chemblmol2 from chemblmol order by molregno asc limit 10; 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select * into chemblmol2 from chemblmol order by molregno as... 210s + ^ 210s CREATE INDEX mol_idx22 ON chemblmol2 using gist(m); 210s +ERROR: relation "chemblmol2" does not exist 210s -- start with a direct seq scan to verify that there is a result 210s SET enable_indexscan=off; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s select count(*) from chemblmol where m@='Cc1cc(-n2ncc(=O)[nH]c2=O)ccc1C(=O)c1ccccc1Cl'::mol; 210s - count 210s -------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol where m@='Cc1cc(-n2ncc(=O)[nH... 210s + ^ 210s select count(*) from chemblmol join chemblmol2 using (m); 210s - count 210s -------- 210s - 10 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol join chemblmol2 using (m); 210s + ^ 210s set rdkit.do_chiral_sss=true; 210s select count(*) from chemblmol c2 join chemblmol using (m); 210s - count 210s -------- 210s - 100 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol c2 join chemblmol using (m); 210s + ^ 210s set rdkit.do_chiral_sss=false; 210s select count(*) from chemblmol c2 join chemblmol using (m); 210s - count 210s -------- 210s - 104 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol c2 join chemblmol using (m); 210s + ^ 210s -- now enable the index to trigger the bug: 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s select count(*) from chemblmol where m@='Cc1cc(-n2ncc(=O)[nH]c2=O)ccc1C(=O)c1ccccc1Cl'::mol; 210s - count 210s -------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol where m@='Cc1cc(-n2ncc(=O)[nH... 210s + ^ 210s select count(*) from chemblmol join chemblmol2 using (m); 210s - count 210s -------- 210s - 10 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol join chemblmol2 using (m); 210s + ^ 210s set rdkit.do_chiral_sss=true; 210s select count(*) from chemblmol c2 join chemblmol using (m); 210s - count 210s -------- 210s - 100 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol c2 join chemblmol using (m); 210s + ^ 210s set rdkit.do_chiral_sss=false; 210s select count(*) from chemblmol c2 join chemblmol using (m); 210s - count 210s -------- 210s - 104 210s -(1 row) 210s - 210s +ERROR: relation "chemblmol" does not exist 210s +LINE 1: select count(*) from chemblmol c2 join chemblmol using (m); 210s + ^ 210s -- build index on qmols 210s CREATE TABLE pgqmol (id int, m qmol); 210s +ERROR: type "qmol" does not exist 210s +LINE 1: CREATE TABLE pgqmol (id int, m qmol); 210s + ^ 210s \copy pgqmol from 'data/qmol_data' 210s +ERROR: relation "pgqmol" does not exist 210s CREATE INDEX molidx ON pgqmol USING gist (m); 210s +ERROR: relation "pgqmol" does not exist 210s SET rdkit.tanimoto_threshold = 0.8; 210s SET rdkit.dice_threshold = 0.8; 210s SET enable_indexscan=off; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s SELECT count(*) FROM pgqmol WHERE m <@ 'c1ccccc1'; 210s - count 210s -------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE m <@ 'c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE m <@ 'c1cccnc1'; 210s - count 210s -------- 210s - 5 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE m <@ 'c1cccnc1'; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE 'c1ccccc1' @> m; 210s - count 210s -------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE 'c1ccccc1' @> m; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE 'c1cccnc1' @> m; 210s - count 210s -------- 210s - 5 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE 'c1cccnc1' @> m; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE m<@ 'c1ccccc1C(=O)N'; 210s - count 210s -------- 210s - 5 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE m<@ 'c1ccccc1C(=O)N'; 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s SELECT count(*) FROM pgqmol WHERE m <@ 'c1ccccc1'; 210s - count 210s -------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE m <@ 'c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE m <@ 'c1cccnc1'; 210s - count 210s -------- 210s - 5 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE m <@ 'c1cccnc1'; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE 'c1ccccc1' @> m; 210s - count 210s -------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE 'c1ccccc1' @> m; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE 'c1cccnc1' @> m; 210s - count 210s -------- 210s - 5 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE 'c1cccnc1' @> m; 210s + ^ 210s SELECT count(*) FROM pgqmol WHERE m<@ 'c1ccccc1C(=O)N'; 210s - count 210s -------- 210s - 5 210s -(1 row) 210s - 210s +ERROR: relation "pgqmol" does not exist 210s +LINE 1: SELECT count(*) FROM pgqmol WHERE m<@ 'c1ccccc1C(=O)N'; 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX molidx; 210s +ERROR: index "molidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/bfpgist-91.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/bfpgist-91.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/bfpgist-91.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/bfpgist-91.out 2024-11-23 20:44:12.217669501 +0000 210s @@ -1,6 +1,8 @@ 210s SET extra_float_digits=0; 210s CREATE INDEX fpidx ON pgbfp USING gist (f); 210s +ERROR: relation "pgbfp" does not exist 210s CREATE INDEX maccsfpidx ON pgbfp USING gist (maccsf); 210s +ERROR: relation "pgbfp" does not exist 210s SET rdkit.tanimoto_threshold = 0.5; 210s SET rdkit.dice_threshold = 0.6; 210s SET enable_indexscan=off; 210s @@ -12,39 +14,27 @@ 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, dice_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml 210s FROM 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s ---------+------------------- 210s - 698576 | 0.604972375690608 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml 210s FROM 210s pgbfp 210s WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----------+------------------- 210s - 2055076 | 0.740740740740741 210s - 5281628 | 0.65625 210s - 10560368 | 0.571428571428571 210s - 755497 | 0.527777777777778 210s - 718644 | 0.526315789473684 210s - 902176 | 0.516129032258065 210s - 687554 | 0.5 210s - 1380883 | 0.5 210s -(8 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s @@ -54,39 +44,27 @@ 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, dice_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml 210s FROM 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s ---------+------------------- 210s - 698576 | 0.604972375690608 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml 210s FROM 210s pgbfp 210s WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----------+------------------- 210s - 2055076 | 0.740740740740741 210s - 5281628 | 0.65625 210s - 10560368 | 0.571428571428571 210s - 755497 | 0.527777777777778 210s - 718644 | 0.526315789473684 210s - 902176 | 0.516129032258065 210s - 687554 | 0.5 210s - 1380883 | 0.5 210s -(8 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s @@ -96,27 +74,19 @@ 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f 210s ORDER BY rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) <%> f,id limit 10; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml 210s FROM 210s pgbfp 210s WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----------+------------------- 210s - 2055076 | 0.740740740740741 210s - 5281628 | 0.65625 210s - 10560368 | 0.571428571428571 210s - 755497 | 0.527777777777778 210s - 718644 | 0.526315789473684 210s - 902176 | 0.516129032258065 210s - 687554 | 0.5 210s - 1380883 | 0.5 210s -(8 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s DROP INDEX fpidx; 210s +ERROR: index "fpidx" does not exist 210s DROP INDEX maccsfpidx; 210s +ERROR: index "maccsfpidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/bfpgin.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/bfpgin.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/bfpgin.out 2024-11-23 20:43:25.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/bfpgin.out 2024-11-23 20:44:12.243659268 +0000 210s @@ -1,5 +1,7 @@ 210s CREATE INDEX fpidx ON pgbfp USING gin (f); 210s +ERROR: relation "pgbfp" does not exist 210s CREATE INDEX maccsfpidx ON pgbfp USING gin (maccsf); 210s +ERROR: relation "pgbfp" does not exist 210s SET rdkit.tanimoto_threshold = 0.5; 210s SET rdkit.dice_threshold = 0.6; 210s SET extra_float_digits=0; 210s @@ -12,39 +14,27 @@ 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, dice_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml 210s FROM 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s ---------+------------------- 210s - 698576 | 0.604972375690608 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml 210s FROM 210s pgbfp 210s WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----------+------------------- 210s - 2055076 | 0.740740740740741 210s - 5281628 | 0.65625 210s - 10560368 | 0.571428571428571 210s - 755497 | 0.527777777777778 210s - 718644 | 0.526315789473684 210s - 902176 | 0.516129032258065 210s - 687554 | 0.5 210s - 1380883 | 0.5 210s -(8 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s @@ -54,39 +44,27 @@ 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, dice_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml 210s FROM 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s ---------+------------------- 210s - 698576 | 0.604972375690608 210s -(1 row) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SELECT 210s id, tanimoto_sml(maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), maccsf) AS sml 210s FROM 210s pgbfp 210s WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----------+------------------- 210s - 2055076 | 0.740740740740741 210s - 5281628 | 0.65625 210s - 10560368 | 0.571428571428571 210s - 755497 | 0.527777777777778 210s - 718644 | 0.526315789473684 210s - 902176 | 0.516129032258065 210s - 687554 | 0.5 210s - 1380883 | 0.5 210s -(8 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s @@ -96,17 +74,10 @@ 210s pgbfp 210s WHERE maccs_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % maccsf 210s ORDER BY sml DESC, id limit 10; 210s - id | sml 210s -----------+------------------- 210s - 2055076 | 0.740740740740741 210s - 5281628 | 0.65625 210s - 10560368 | 0.571428571428571 210s - 755497 | 0.527777777777778 210s - 718644 | 0.526315789473684 210s - 902176 | 0.516129032258065 210s - 687554 | 0.5 210s - 1380883 | 0.5 210s -(8 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s DROP INDEX fpidx; 210s +ERROR: index "fpidx" does not exist 210s DROP INDEX maccsfpidx; 210s +ERROR: index "maccsfpidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/sfpgist.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/sfpgist.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/sfpgist.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/sfpgist.out 2024-11-23 20:44:12.269649036 +0000 210s @@ -1,5 +1,6 @@ 210s SET extra_float_digits=0; 210s CREATE INDEX fpidx ON pgsfp USING gist (f); 210s +ERROR: relation "pgsfp" does not exist 210s SET rdkit.tanimoto_threshold = 0.6; 210s SET rdkit.dice_threshold = 0.6; 210s SET enable_indexscan=off; 210s @@ -11,38 +12,18 @@ 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f 210s ORDER BY sml DESC, id; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SELECT 210s id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml 210s FROM 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f 210s ORDER BY sml DESC, id; 210s - id | sml 210s ----------+------------------- 210s - 659725 | 0.685714285714286 210s - 63248 | 0.648648648648649 210s - 6266272 | 0.641025641025641 210s - 5359275 | 0.638888888888889 210s - 5718138 | 0.638888888888889 210s - 917183 | 0.628571428571429 210s - 161167 | 0.621621621621622 210s - 230488 | 0.621621621621622 210s - 328013 | 0.621621621621622 210s - 564008 | 0.619047619047619 210s - 2910597 | 0.615384615384615 210s - 3963948 | 0.615384615384615 210s - 5407397 | 0.615384615384615 210s - 3784792 | 0.613636363636364 210s - 3096571 | 0.609756097560976 210s - 801655 | 0.605263157894737 210s - 3157044 | 0.605263157894737 210s - 807628 | 0.6 210s -(18 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s @@ -52,39 +33,20 @@ 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f 210s ORDER BY sml DESC, id; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SELECT 210s id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml 210s FROM 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f 210s ORDER BY sml DESC, id; 210s - id | sml 210s ----------+------------------- 210s - 659725 | 0.685714285714286 210s - 63248 | 0.648648648648649 210s - 6266272 | 0.641025641025641 210s - 5359275 | 0.638888888888889 210s - 5718138 | 0.638888888888889 210s - 917183 | 0.628571428571429 210s - 161167 | 0.621621621621622 210s - 230488 | 0.621621621621622 210s - 328013 | 0.621621621621622 210s - 564008 | 0.619047619047619 210s - 2910597 | 0.615384615384615 210s - 3963948 | 0.615384615384615 210s - 5407397 | 0.615384615384615 210s - 3784792 | 0.613636363636364 210s - 3096571 | 0.609756097560976 210s - 801655 | 0.605263157894737 210s - 3157044 | 0.605263157894737 210s - 807628 | 0.6 210s -(18 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX fpidx; 210s +ERROR: index "fpidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/slfpgist.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/slfpgist.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/slfpgist.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/slfpgist.out 2024-11-23 20:44:12.295638803 +0000 210s @@ -1,5 +1,6 @@ 210s SET extra_float_digits=0; 210s CREATE INDEX fpidx ON pgsfp USING gist (f gist_sfp_low_ops); 210s +ERROR: relation "pgsfp" does not exist 210s SET rdkit.tanimoto_threshold = 0.6; 210s SET rdkit.dice_threshold = 0.6; 210s SET enable_indexscan=off; 210s @@ -11,38 +12,18 @@ 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f 210s ORDER BY sml DESC, id; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SELECT 210s id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml 210s FROM 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f 210s ORDER BY sml DESC, id; 210s - id | sml 210s ----------+------------------- 210s - 659725 | 0.685714285714286 210s - 63248 | 0.648648648648649 210s - 6266272 | 0.641025641025641 210s - 5359275 | 0.638888888888889 210s - 5718138 | 0.638888888888889 210s - 917183 | 0.628571428571429 210s - 161167 | 0.621621621621622 210s - 230488 | 0.621621621621622 210s - 328013 | 0.621621621621622 210s - 564008 | 0.619047619047619 210s - 2910597 | 0.615384615384615 210s - 3963948 | 0.615384615384615 210s - 5407397 | 0.615384615384615 210s - 3784792 | 0.613636363636364 210s - 3096571 | 0.609756097560976 210s - 801655 | 0.605263157894737 210s - 3157044 | 0.605263157894737 210s - 807628 | 0.6 210s -(18 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s @@ -52,39 +33,20 @@ 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) % f 210s ORDER BY sml DESC, id; 210s - id | sml 210s -----+----- 210s -(0 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SELECT 210s id, dice_sml(morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1), f) AS sml 210s FROM 210s pgsfp 210s WHERE morgan_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol, 1) # f 210s ORDER BY sml DESC, id; 210s - id | sml 210s ----------+------------------- 210s - 659725 | 0.685714285714286 210s - 63248 | 0.648648648648649 210s - 6266272 | 0.641025641025641 210s - 5359275 | 0.638888888888889 210s - 5718138 | 0.638888888888889 210s - 917183 | 0.628571428571429 210s - 161167 | 0.621621621621622 210s - 230488 | 0.621621621621622 210s - 328013 | 0.621621621621622 210s - 564008 | 0.619047619047619 210s - 2910597 | 0.615384615384615 210s - 3963948 | 0.615384615384615 210s - 5407397 | 0.615384615384615 210s - 3784792 | 0.613636363636364 210s - 3096571 | 0.609756097560976 210s - 801655 | 0.605263157894737 210s - 3157044 | 0.605263157894737 210s - 807628 | 0.6 210s -(18 rows) 210s - 210s +ERROR: relation "pgsfp" does not exist 210s +LINE 4: pgsfp 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX fpidx; 210s +ERROR: index "fpidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/fps.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/fps.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/fps.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/fps.out 2024-11-23 20:44:12.325626997 +0000 210s @@ -1,100 +1,68 @@ 210s SET extra_float_digits=0; 210s SELECT dice_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol)); 210s - dice_sml 210s -------------------- 210s - 0.372093023255814 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1... 210s + ^ 210s SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol),0.5,0.5); 210s - tversky_sml 210s -------------------- 210s - 0.372093023255814 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccn... 210s + ^ 210s SELECT tanimoto_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol)); 210s - tanimoto_sml 210s -------------------- 210s - 0.228571428571429 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT tanimoto_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1cc... 210s + ^ 210s SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccncc1'::mol),1.0,1.0); 210s - tversky_sml 210s -------------------- 210s - 0.228571428571429 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT tversky_sml(rdkit_fp('c1ccccc1'::mol),rdkit_fp('c1ccn... 210s + ^ 210s SELECT dice_sml(atompair_fp('c1ccccc1'::mol),atompair_fp('c1ccncc1'::mol)); 210s - dice_sml 210s -------------------- 210s - 0.666666666666667 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(atompair_fp('c1ccccc1'::mol),atompair_fp('c1... 210s + ^ 210s SELECT dice_sml(torsion_fp('c1ccccc1'::mol),torsion_fp('c1ccncc1'::mol)); 210s - dice_sml 210s -------------------- 210s - 0.333333333333333 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(torsion_fp('c1ccccc1'::mol),torsion_fp('c1cc... 210s + ^ 210s SELECT dice_sml(morgan_fp('c1ccccc1'::mol,2),morgan_fp('c1ccncc1'::mol,2)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(morgan_fp('c1ccccc1'::mol,2),morgan_fp('c1cc... 210s + ^ 210s SELECT dice_sml(morgan_fp('c1ccccc1'::mol),morgan_fp('c1ccncc1'::mol)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(morgan_fp('c1ccccc1'::mol),morgan_fp('c1ccnc... 210s + ^ 210s SELECT dice_sml(morganbv_fp('c1ccccc1'::mol,2),morganbv_fp('c1ccncc1'::mol,2)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(morganbv_fp('c1ccccc1'::mol,2),morganbv_fp('... 210s + ^ 210s SELECT dice_sml(morganbv_fp('c1ccccc1'::mol),morganbv_fp('c1ccncc1'::mol)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(morganbv_fp('c1ccccc1'::mol),morganbv_fp('c1... 210s + ^ 210s SELECT dice_sml(featmorgan_fp('c1ccccc1'::mol,2),featmorgan_fp('c1ccncc1'::mol,2)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(featmorgan_fp('c1ccccc1'::mol,2),featmorgan_... 210s + ^ 210s SELECT dice_sml(featmorgan_fp('c1ccccc1'::mol),featmorgan_fp('c1ccncc1'::mol)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(featmorgan_fp('c1ccccc1'::mol),featmorgan_fp... 210s + ^ 210s SELECT dice_sml(featmorganbv_fp('c1ccccc1'::mol,2),featmorganbv_fp('c1ccncc1'::mol,2)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(featmorganbv_fp('c1ccccc1'::mol,2),featmorga... 210s + ^ 210s SELECT dice_sml(featmorganbv_fp('c1ccccc1'::mol),featmorganbv_fp('c1ccncc1'::mol)); 210s - dice_sml 210s ----------- 210s - 0.5 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(featmorganbv_fp('c1ccccc1'::mol),featmorganb... 210s + ^ 210s SELECT tanimoto_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1ccncc1'::mol)); 210s - tanimoto_sml 210s --------------- 210s - 0.375 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT tanimoto_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1cc... 210s + ^ 210s SELECT dice_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1ccncc1'::mol)); 210s - dice_sml 210s -------------------- 210s - 0.545454545454545 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: SELECT dice_sml(maccs_fp('c1ccccc1'::mol),maccs_fp('c1ccncc1... 210s + ^ 210s SET rdkit.tanimoto_threshold = 0.4; 210s SELECT 210s id, tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml 210s @@ -102,20 +70,9 @@ 210s pgbfp 210s WHERE rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) % f 210s ORDER BY sml DESC, id LIMIT 10; 210s - id | sml 210s -----------+------------------- 210s - 698576 | 0.433663366336634 210s - 16000816 | 0.423290203327172 210s - 1959267 | 0.422750424448217 210s - 576770 | 0.422310756972112 210s - 16746067 | 0.420439844760673 210s - 5770965 | 0.412478336221837 210s - 24747640 | 0.412371134020619 210s - 15945163 | 0.409246575342466 210s - 5770966 | 0.408839779005525 210s - 690546 | 0.408759124087591 210s -(10 rows) 210s - 210s +ERROR: relation "pgbfp" does not exist 210s +LINE 4: pgbfp 210s + ^ 210s SET rdkit.tanimoto_threshold = 0.5; 210s SET rdkit.dice_threshold = 0.5; 210s SELECT 210s @@ -124,148 +81,99 @@ 210s pgtorsfp 210s WHERE torsion_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f 210s ORDER BY sml DESC, id; 210s - id | sml 210s ----------+----- 210s - 3790017 | 0.5 210s -(1 row) 210s - 210s +ERROR: relation "pgtorsfp" does not exist 210s +LINE 4: pgtorsfp 210s + ^ 210s SELECT 210s id, dice_sml(atompair_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), f) AS sml 210s FROM 210s pgpairfp 210s WHERE atompair_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol) # f 210s ORDER BY sml DESC, id LIMIT 10; 210s - id | sml 210s -----------+------------------- 210s - 659725 | 0.636678200692042 210s - 917183 | 0.595155709342561 210s - 10713707 | 0.595092024539877 210s - 3790017 | 0.588555858310627 210s - 230488 | 0.576687116564417 210s - 16193886 | 0.55012853470437 210s - 3236648 | 0.5390625 210s - 5359275 | 0.534201954397394 210s - 6213987 | 0.532871972318339 210s - 161167 | 0.52760736196319 210s -(10 rows) 210s - 210s +ERROR: relation "pgpairfp" does not exist 210s +LINE 4: pgpairfp 210s + ^ 210s select tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdkit_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.315398886827458 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ..._sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdki... 210s + ^ 210s set rdkit.rdkit_fp_size = 512; 210s select tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdkit_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s ------------------- 210s - 0.47103274559194 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ..._sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdki... 210s + ^ 210s set rdkit.rdkit_fp_size = 1024; 210s select tanimoto_sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdkit_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.315398886827458 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ..._sml(rdkit_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), rdki... 210s + ^ 210s select tanimoto_sml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), layered_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.724941724941725 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), laye... 210s + ^ 210s set rdkit.layered_fp_size = 512; 210s select tanimoto_sml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), layered_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.788235294117647 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), laye... 210s + ^ 210s set rdkit.layered_fp_size = 1024; 210s select tanimoto_sml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), layered_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.724941724941725 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ml(layered_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), laye... 210s + ^ 210s select tanimoto_sml(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------- 210s - 0.325 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...l(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morg... 210s + ^ 210s set rdkit.morgan_fp_size = 512; 210s select tanimoto_sml(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------- 210s - 0.325 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...l(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morg... 210s + ^ 210s set rdkit.morgan_fp_size = 1024; 210s select tanimoto_sml(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.317073170731707 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...l(morganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), morg... 210s + ^ 210s select tanimoto_sml(featmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), featmorganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.205882352941176 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...atmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), feat... 210s + ^ 210s set rdkit.featmorgan_fp_size = 512; 210s select tanimoto_sml(featmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), featmorganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.205882352941176 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...atmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), feat... 210s + ^ 210s set rdkit.featmorgan_fp_size = 1024; 210s select tanimoto_sml(featmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), featmorganbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.205882352941176 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...atmorganbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), feat... 210s + ^ 210s select tanimoto_sml(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), torsionbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.454545454545455 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), tors... 210s + ^ 210s set rdkit.hashed_torsion_fp_size = 512; 210s select tanimoto_sml(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), torsionbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.476190476190476 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), tors... 210s + ^ 210s set rdkit.hashed_torsion_fp_size = 1024; 210s select tanimoto_sml(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), torsionbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.454545454545455 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...(torsionbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), tors... 210s + ^ 210s select tanimoto_sml(atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atompairbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s ------------------- 210s - 0.56198347107438 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atom... 210s + ^ 210s set rdkit.hashed_atompair_fp_size = 512; 210s select tanimoto_sml(atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atompairbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.582608695652174 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atom... 210s + ^ 210s set rdkit.hashed_atompair_fp_size = 1024; 210s select tanimoto_sml(atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atompairbv_fp('N=C1CC(NC2=CC=CC=C12)C1=CC=CC=C1'::mol)) AS sml; 210s - sml 210s -------------------- 210s - 0.571428571428571 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...atompairbv_fp('O=C1CC(OC2=CC=CC=C12)C1=CC=CC=C1'::mol), atom... 210s + ^ 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/reaction.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/reaction.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/reaction.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/reaction.out 2024-11-23 20:44:12.368610074 +0000 210s @@ -1,5 +1,9 @@ 210s SET extra_float_digits=0; 210s PREPARE dummy AS SELECT rdkit_version(); 210s +ERROR: function rdkit_version() does not exist 210s +LINE 1: PREPARE dummy AS SELECT rdkit_version(); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.ignore_reaction_agents=false; 210s SET rdkit.agent_FP_bit_ratio=0.2; 210s SET rdkit.difference_FP_weight_agents=1; 210s @@ -8,158 +12,96 @@ 210s SET rdkit.threshold_unmapped_reactant_atoms=0.2; 210s SET rdkit.init_reaction=true; 210s SELECT reaction_from_smiles('c1ccccc1>>c1cccnc1'); 210s - reaction_from_smiles 210s ----------------------- 210s - c1ccccc1>>c1ccncc1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_from_smiles('c1ccccc1>>c1cccnc1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_from_smiles('c1ccccc1>CC(=O)O>c1cccnc1'); 210s - reaction_from_smiles 210s ---------------------------- 210s - c1ccccc1>CC(=O)O>c1ccncc1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_from_smiles('c1ccccc1>CC(=O)O>c1cccnc1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_from_smarts('[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]'); 210s - reaction_from_smarts 210s -------------------------------------------------------------------- 210s - c([c:4][c:3][c:2][c:1])[c:5]>CC(O)=O>n([c:4][c:3][c:2][c:1])[c:5] 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_from_smarts('[c1:1][c:2][c:3][c:4]c[c1:5]>CC... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]'); 210s - reaction_from_smarts 210s --------------------------------------------------------------------------- 210s - c([c:4][c:3][c:2][c:1])[c:5]>CC(O)=O.FC(F)F>n([c:4][c:3][c:2][c:1])[c:5] 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1'); 210s - reaction_from_smarts 210s ----------------------- 210s - *1ccccc1>>c1cnccn1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_to_smiles(reaction_from_smiles('c1ccccc1>>c1cccnc1')); 210s - reaction_to_smiles 210s --------------------- 210s - c1ccccc1>>c1ccncc1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_to_smiles(reaction_from_smiles('c1ccccc1>>c1... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_to_smiles(reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1')); 210s - reaction_to_smiles 210s --------------------- 210s - *1ccccc1>>c1cnccn1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_to_smiles(reaction_from_smarts('c1ccc[n,c]c1... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_to_smarts(reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1')); 210s - reaction_to_smarts 210s ------------------------- 210s - c1ccc[n,c]c1>>c1nccnc1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_to_smarts(reaction_from_smarts('c1ccc[n,c]c1... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_to_smarts('c1cccnc1>>c1nccnc1'::reaction); 210s - reaction_to_smarts 210s --------------------------------------------------------------------- 210s - [#6]1:[#6]:[#6]:[#6]:[#7]:[#6]:1>>[#6]1:[#7]:[#6]:[#6]:[#7]:[#6]:1 210s -(1 row) 210s - 210s +ERROR: type "reaction" does not exist 210s +LINE 1: SELECT reaction_to_smarts('c1cccnc1>>c1nccnc1'::reaction); 210s + ^ 210s SELECT reaction_to_ctab(reaction_from_smiles('c1ccccc1>>c1cccnc1')); 210s - reaction_to_ctab 210s ------------------------------------------------------------------------ 210s - $RXN + 210s - + 210s - RDKit + 210s - + 210s - 1 1 + 210s - $MOL + 210s - + 210s - RDKit 2D + 210s - + 210s - 6 6 0 0 0 0 0 0 0 0999 V2000 + 210s - 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1 2 4 0 + 210s - 2 3 4 0 + 210s - 3 4 4 0 + 210s - 4 5 4 0 + 210s - 5 6 4 0 + 210s - 6 1 4 0 + 210s - M END + 210s - $MOL + 210s - + 210s - RDKit 2D + 210s - + 210s - 6 6 0 0 0 0 0 0 0 0999 V2000 + 210s - 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - -0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0+ 210s - 1 2 4 0 + 210s - 2 3 4 0 + 210s - 3 4 4 0 + 210s - 4 5 4 0 + 210s - 5 6 4 0 + 210s - 6 1 4 0 + 210s - M END + 210s - 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_to_ctab(reaction_from_smiles('c1ccccc1>>c1cc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_numreactants(reaction_from_smiles('[Cl].c1ccccc1>>c1cccnc1.[OH2]')); 210s - reaction_numreactants 210s ------------------------ 210s - 2 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_numreactants(reaction_from_smiles('[Cl].c1cc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_numproducts(reaction_from_smiles('[Cl].c1ccccc1>>c1cccnc1.[OH2]')); 210s - reaction_numproducts 210s ----------------------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_numproducts(reaction_from_smiles('[Cl].c1ccc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_numagents(reaction_from_smiles('[Cl].c1ccccc1>CC(=O)O.[Na+]>c1cccnc1.[OH2]')); 210s - reaction_numagents 210s --------------------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smiles(unknown) does not exist 210s +LINE 1: SELECT reaction_numagents(reaction_from_smiles('[Cl].c1ccccc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]')); 210s - reaction_numagents 210s --------------------- 210s - 2 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.move_unmmapped_reactants_to_agents=false; 210s SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]')); 210s - reaction_numagents 210s --------------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.move_unmmapped_reactants_to_agents=true; 210s SET rdkit.threshold_unmapped_reactant_atoms=0.9; 210s SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1:1][c:2][c:3][c:4]c[c1:5]>CC(=O)O>[c1:1][c:2][c:3][c:4]n[c1:5]')); 210s - reaction_numagents 210s --------------------- 210s - 3 210s -(1 row) 210s - 210s +ERROR: function reaction_from_smarts(unknown) does not exist 210s +LINE 1: SELECT reaction_numagents(reaction_from_smarts('C(F)(F)F.[c1... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.threshold_unmapped_reactant_atoms=0.2; 210s SELECT 'c1ccccc1>>c1cccnc1'::reaction @= 'c1ccccc1>>c1cccnc1'::reaction; 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "reaction" does not exist 210s +LINE 1: SELECT 'c1ccccc1>>c1cccnc1'::reaction @= 'c1ccccc1>>c1cccnc1... 210s + ^ 210s SELECT 'c1ccccc1>>c1cccnc1'::reaction @= 'c1ccccc1>>c1cncnc1'::reaction; 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "reaction" does not exist 210s +LINE 1: SELECT 'c1ccccc1>>c1cccnc1'::reaction @= 'c1ccccc1>>c1cncnc1... 210s + ^ 210s SELECT reaction_from_ctab('$RXN 210s 210s RDKit 210s @@ -201,742 +143,583 @@ 210s 5 6 4 0 210s 6 1 4 0 210s M END'); 210s - reaction_from_ctab 210s --------------------------------- 210s - C1:C:C:C:C:C:1>>C1:C:C:N:C:C:1 210s -(1 row) 210s - 210s +ERROR: function reaction_from_ctab(unknown) does not exist 210s +LINE 1: SELECT reaction_from_ctab('$RXN ... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s CREATE TABLE tmp (id integer, tmprxn text); 210s \copy tmp from 'data/reaction_test_data.out.rsmi'; 210s select * into pgreactions from (select id,reaction_from_smiles(tmprxn::cstring) rxn from tmp) as r where r is not null; 210s +ERROR: function reaction_from_smiles(cstring) does not exist 210s +LINE 1: select * into pgreactions from (select id,reaction_from_smil... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.move_unmmapped_reactants_to_agents=false; 210s select * into pgreactions_unchanged from (select id,reaction_from_smiles(tmprxn::cstring) rxn from tmp) as r where r is not null; 210s +ERROR: function reaction_from_smiles(cstring) does not exist 210s +LINE 1: ...lect * into pgreactions_unchanged from (select id,reaction_f... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s DROP table tmp; 210s SET rdkit.move_unmmapped_reactants_to_agents=true; 210s SELECT count(*) FROM pgreactions; 210s - count 210s -------- 210s - 1000 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions; 210s + ^ 210s SELECT count(*) FROM pgreactions_unchanged; 210s - count 210s -------- 210s - 1000 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions_unchanged" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions_unchanged; 210s + ^ 210s SELECT SUM(reaction_numreactants(rxn)) FROM pgreactions; 210s - sum 210s ------- 210s - 1898 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT SUM(reaction_numreactants(rxn)) FROM pgreactions; 210s + ^ 210s SELECT SUM(reaction_numreactants(rxn)) FROM pgreactions_unchanged; 210s - sum 210s ------- 210s - 3517 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions_unchanged" does not exist 210s +LINE 1: SELECT SUM(reaction_numreactants(rxn)) FROM pgreactions_unch... 210s + ^ 210s SELECT SUM(reaction_numproducts(rxn)) FROM pgreactions; 210s - sum 210s ------- 210s - 1157 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT SUM(reaction_numproducts(rxn)) FROM pgreactions; 210s + ^ 210s SELECT SUM(reaction_numproducts(rxn)) FROM pgreactions_unchanged; 210s - sum 210s ------- 210s - 1157 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions_unchanged" does not exist 210s +LINE 1: SELECT SUM(reaction_numproducts(rxn)) FROM pgreactions_uncha... 210s + ^ 210s SELECT SUM(reaction_numagents(rxn)) FROM pgreactions; 210s - sum 210s ------- 210s - 2528 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT SUM(reaction_numagents(rxn)) FROM pgreactions; 210s + ^ 210s SELECT SUM(reaction_numagents(rxn)) FROM pgreactions_unchanged; 210s - sum 210s ------ 210s - 909 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions_unchanged" does not exist 210s +LINE 1: SELECT SUM(reaction_numagents(rxn)) FROM pgreactions_unchang... 210s + ^ 210s CREATE INDEX rxnidx ON pgreactions USING gist(rxn); 210s +ERROR: relation "pgreactions" does not exist 210s SET enable_indexscan=off; 210s SET enable_bitmapscan=off; 210s SET enable_seqscan=on; 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>c1ccncc1'; 210s - count 210s -------- 210s - 47 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>c1ccn... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>c1ccccc1'; 210s - count 210s -------- 210s - 50 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>c1ccc... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'<@rxn; 210s - count 210s -------- 210s - 47 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'<... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'<@rxn; 210s - count 210s -------- 210s - 50 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'<... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>'; 210s - count 210s -------- 210s - 667 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>'; 210s - count 210s -------- 210s - 83 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'<@rxn; 210s - count 210s -------- 210s - 667 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>'<@rxn; 210s - count 210s -------- 210s - 83 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccncc1'; 210s - count 210s -------- 210s - 79 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccncc1'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccccc1'; 210s - count 210s -------- 210s - 650 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'<@rxn; 210s - count 210s -------- 210s - 79 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE '>>c1ccccc1'<@rxn; 210s - count 210s -------- 210s - 650 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE '>>c1ccccc1'<@rxn; 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=off; 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>c1ccncc1'; 210s - count 210s -------- 210s - 47 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>c1ccn... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>c1ccccc1'; 210s - count 210s -------- 210s - 50 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>c1ccc... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'<@rxn; 210s - count 210s -------- 210s - 47 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'<... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'<@rxn; 210s - count 210s -------- 210s - 50 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'<... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>'; 210s - count 210s -------- 210s - 667 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1ccccc1>>'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>'; 210s - count 210s -------- 210s - 83 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'c1cnccc1>>'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'<@rxn; 210s - count 210s -------- 210s - 667 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>'<@rxn; 210s - count 210s -------- 210s - 83 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccncc1'; 210s - count 210s -------- 210s - 79 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccncc1'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccccc1'; 210s - count 210s -------- 210s - 650 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn@>'>>c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'<@rxn; 210s - count 210s -------- 210s - 79 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE '>>c1ccccc1'<@rxn; 210s - count 210s -------- 210s - 650 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE '>>c1ccccc1'<@rxn; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn?>'c1ccccc1>>c1ccncc1'; 210s - count 210s -------- 210s - 47 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn?>'c1ccccc1>>c1ccn... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn?>'c1cnccc1>>c1ccccc1'; 210s - count 210s -------- 210s - 50 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn?>'c1cnccc1>>c1ccc... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>c1ccncc1'?>c1ccncc1'?... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1cnccc1>>c1ccccc1'?>c1ccccc1'?... 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn?>'c1ccccc1>>'; 210s - count 210s -------- 210s - 667 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn?>'c1ccccc1>>'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn?>'c1cnccc1>>'; 210s - count 210s -------- 210s - 83 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn?>'c1cnccc1>>'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE 'c1ccccc1>>'?>'?>'?>'?'>>c1ccncc1'; 210s - count 210s -------- 210s - 79 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn?>'>>c1ccncc1'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE rxn?>'>>c1ccccc1'; 210s - count 210s -------- 210s - 650 210s -(1 row) 210s - 210s +ERROR: relation "pgreactions" does not exist 210s +LINE 1: SELECT count(*) FROM pgreactions WHERE rxn?>'>>c1ccccc1'; 210s + ^ 210s SELECT count(*) FROM pgreactions WHERE '>>c1ccncc1'?>c1ccncc1'?>c1ccccc1'?>c1ccccc1'?>c1ccncc1',1), reaction_difference_fp('c1ccccc1>>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ncccc1>>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.636363636363636 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.603448275862069 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ccccc1>>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ncccc1>>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.2 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.2 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ccccc1>>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ncccc1>>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.454545454545455 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.444933920704846 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.620689655172414 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.514285714285714 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.4 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.4 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.409090909090909 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',3)); 210s - tanimoto_sml 210s ------------------- 210s - 0.32258064516129 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>>c1ccncc1',4)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>>c1ncncc1',4)); 210s - tanimoto_sml 210s ------------------- 210s - 0.27710843373494 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',4)); 210s - tanimoto_sml 210s -------------------- 210s - 0.237113402061856 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>>c1ccncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>>c1ncncc1',5)); 210s - tanimoto_sml 210s -------------------- 210s - 0.793388429752066 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',5)); 210s - tanimoto_sml 210s -------------------- 210s - 0.604938271604938 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.agent_FP_bit_ratio=0.5; 210s SET rdkit.difference_FP_weight_agents=-3; 210s SET rdkit.difference_FP_weight_nonagents=7; 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ccccc1>>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ncccc1>>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.636363636363636 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.515789473684211 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ccccc1>>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',2), reaction_difference_fp('c1ncccc1>>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.2 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.2 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ccccc1>>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',3), reaction_difference_fp('c1ncccc1>>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.454545454545455 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.403314917127072 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.620689655172414 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.514285714285714 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.4 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',2), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',2)); 210s - tanimoto_sml 210s --------------- 210s - 0.4 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.428571428571429 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',3), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',3)); 210s - tanimoto_sml 210s -------------------- 210s - 0.344827586206897 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>>c1ccncc1',4)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>>c1ncncc1',4)); 210s - tanimoto_sml 210s -------------------- 210s - 0.285714285714286 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',4), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',4)); 210s - tanimoto_sml 210s -------------------- 210s - 0.244897959183673 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>>c1ccncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>>c1ncncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 0.8 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',5)); 210s - tanimoto_sml 210s -------------------- 210s - 0.608695652173913 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SET rdkit.ignore_reaction_agents=true; 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ccccc1>>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccncc1',1), reaction_difference_fp('c1ncccc1>>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.636363636363636 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>>c1ccnc... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',1), reaction_difference_fp('c1ncccc1>[Na+]>c1ncncc1',1)); 210s - tanimoto_sml 210s -------------------- 210s - 0.636363636363636 210s -(1 row) 210s - 210s +ERROR: function reaction_difference_fp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_difference_fp('c1ccccc1>CC(=O)O... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>>c1ccncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>>c1ncncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 0.8 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>>c1ccn... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 1 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)O.[Na+]>c1ccncc1',5), reaction_structural_bfp('c1ncccc1>[Na+]>c1ncncc1',5)); 210s - tanimoto_sml 210s --------------- 210s - 0.8 210s -(1 row) 210s - 210s +ERROR: function reaction_structural_bfp(unknown, integer) does not exist 210s +LINE 1: SELECT tanimoto_sml(reaction_structural_bfp('c1ccccc1>CC(=O)... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s SELECT substring(reaction_to_svg('[C:1][O:2].[C:3][C:4]>>[C:1][O:2][C:3][C:4]'::reaction)::text,1,120) svg; 210s - svg 210s ---------------------------------------------- 210s - + 210s - >[C:1][O:2][C:3][C:4]'::reaction):... 210s + ^ 210s SELECT substring(reaction_to_svg('[C:1][O:2].[C:3][C:4]>>[C:1][O:2][C:3][C:4]'::reaction, true)::text,1,120) svg; 210s - svg 210s ---------------------------------------------- 210s - + 210s - >[C:1][O:2][C:3][C:4]'::reaction, ... 210s + ^ 210s SET enable_indexscan=on; 210s SET enable_bitmapscan=on; 210s SET enable_seqscan=on; 210s DROP INDEX rxnidx; 210s +ERROR: index "rxnidx" does not exist 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/fmcs.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/fmcs.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/fmcs.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/fmcs.out 2024-11-23 20:44:12.397598661 +0000 210s @@ -1,23 +1,25 @@ 210s -- github #3687 : crash on bogus fmcs input 210s select fmcs(m::text) from pgmol where m@>'c1ncccc1'; 210s - fmcs 210s ----------------------------------------------- 210s - [#6]1:,-[#7]:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-1 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: select fmcs(m::text) from pgmol where m@>'c1ncccc1'; 210s + ^ 210s select fmcs(m) from pgmol where m@>'c1ncccc1'; 210s - fmcs 210s ----------------------------------------------- 210s - [#6]1:,-[#6]:,-[#6]:,-[#6]:,-[#6]:,-[#7]:,-1 210s -(1 row) 210s - 210s +ERROR: relation "pgmol" does not exist 210s +LINE 1: select fmcs(m) from pgmol where m@>'c1ncccc1'; 210s + ^ 210s -- github #3687 : crash on bogus fmcs input 210s select fmcs('q'); 210s -ERROR: findMCS: could not create molecule from SMILES 'q' 210s -CONTEXT: SQL function "fmcs_smiles" statement 1 210s +ERROR: function fmcs(unknown) does not exist 210s +LINE 1: select fmcs('q'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select fmcs('p'); 210s -ERROR: findMCS: could not create molecule from SMILES 'p' 210s -CONTEXT: SQL function "fmcs_smiles" statement 1 210s +ERROR: function fmcs(unknown) does not exist 210s +LINE 1: select fmcs('p'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select fmcs('C1CC'); 210s -ERROR: findMCS: could not create molecule from SMILES 'C1CC' 210s -CONTEXT: SQL function "fmcs_smiles" statement 1 210s +ERROR: function fmcs(unknown) does not exist 210s +LINE 1: select fmcs('C1CC'); 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/query.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/query.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/query.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/query.out 2024-11-23 20:44:12.420589609 +0000 210s @@ -16,11 +16,10 @@ 210s M V30 END SGROUP 210s M V30 END CTAB 210s M END'), '{"setGenericQueryFromProperties": true, "adjustDegree":false}') <<@ 'c1c(OF)cccc1'; 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_adjust_query_properties(mol_from_ctab('alkquery.m... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select mol_adjust_query_properties(mol_from_ctab('alkquery.mol 210s Generated by WebMolKit 210s 210s @@ -39,11 +38,10 @@ 210s M V30 END SGROUP 210s M V30 END CTAB 210s M END'), '{"setGenericQueryFromProperties": false, "adjustDegree":false}') <@ 'c1c(OF)cccc1'; 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_adjust_query_properties(mol_from_ctab('alkquery.m... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select mol_adjust_query_properties(mol_from_ctab('alkquery.mol 210s Generated by WebMolKit 210s 210s @@ -62,11 +60,10 @@ 210s M V30 END SGROUP 210s M V30 END CTAB 210s M END'), '{"setGenericQueryFromProperties": true, "adjustDegree":false}') <<@ 'c1c(OF)cccc1'; 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_adjust_query_properties(mol_from_ctab('alkquery.m... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s select mol_adjust_query_properties(mol_from_ctab('alkquery.mol 210s Generated by WebMolKit 210s 210s @@ -85,8 +82,7 @@ 210s M V30 END SGROUP 210s M V30 END CTAB 210s M END'), '{"setGenericQueryFromProperties": false, "adjustDegree":false}') <@ 'c1c(OF)cccc1'; 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: function mol_from_ctab(unknown) does not exist 210s +LINE 1: select mol_adjust_query_properties(mol_from_ctab('alkquery.m... 210s + ^ 210s +HINT: No function matches the given name and argument types. You might need to add explicit type casts. 210s diff -U3 /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/xqm.out /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/xqm.out 210s --- /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/expected/xqm.out 2023-12-05 19:34:32.000000000 +0000 210s +++ /tmp/autopkgtest.sGFASs/build.jmP/src/Code/PgSQL/rdkit/results/xqm.out 2024-11-23 20:44:12.446579377 +0000 210s @@ -1,432 +1,150 @@ 210s -- parsing and conversion to text 210s select mol_to_xqmol('Cc1n[nH]c(F)c1'::mol); 210s - mol_to_xqmol 210s ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "3", + 210s - "tautomers": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMGQCgAAAADBAdAKAAAAAMDB2A4AAAAAwEDBkAoAAAAAwQJACAAAAABBkBoAAAAAwMBCwABAAECaAwCA2gMAwRoDAQFAAQGaAwGAWgMFAEAAAAFAQIDBAYXBAAAAAAAAAAW", + 210s - "smiles": "Cc1cc(F)[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMGQCgAAAADBAdAOAAAAAMBAwdgKAAAAAMDBkAoAAAAAwQJACAAAAABBkBoAAAAAwMBCwABAAECaAwCA2gMAwRoDAQFAAQGaAwGAWgMFAEAAAAFAQIDBAYXBAAAAAAAAAAW", + 210s - "smiles": "Cc1cc(F)n[nH]1" + 210s - } + 210s - ], + 210s - "template": { + 210s - "pkl": "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",+ 210s - "smarts": "[#6]-[#6]1-,=,:[#7]:[#7]-,=,:[#6](-[#9])-,=,:[#6]-,=,:1" + 210s - }, + 210s - "modifiedAtoms": [ + 210s - "2", + 210s - "3" + 210s - ], + 210s - "modifiedBonds": [ + 210s - "1", + 210s - "3", + 210s - "5", + 210s - "6" + 210s - ] + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('Cc1n[nH]c(F)c1'::mol); 210s + ^ 210s select mol_to_xqmol('COC |LN:1:1.3|'::mol); 210s - mol_to_xqmol 210s --------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "2", + 210s - "mols": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAADAAAAAgAAAIABBgBoAAAAAAEDCAAoAAAAAAIGAGgAAAAAAQMLAAEAAQIAFwQAAAAAAAAAFg==", + 210s - "smiles": "COC" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAEAAAAAwAAAIABBgBoAAAAAAEDCAAoAAAAAAIIACgAAAAAAgYAaAAAAAABAwsAAQABAgACAwAXBAAAAAAAAAAW", + 210s - "smiles": "COOC" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAFAAAABAAAAIABBgBoAAAAAAEDCAAoAAAAAAIIACgAAAAAAggAKAAAAAACBgBoAAAAAAEDCwABAAECAAIDAAMEABcEAAAAAAAAABY=",+ 210s - "smiles": "COOOC" + 210s - } + 210s - ] + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC |LN:1:1.3|'::mol); 210s + ^ 210s select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s - mol_to_xqmol 210s ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "4", + 210s - "num_entries": "3", + 210s - "tautomerQueries": [ + 210s - { + 210s - "tautomers": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBoAAAAAAEDCAAoAAAAAAIGQCgAAAAABAdAKAAAAAMDBkBoAAAAAwMBB0A4AAAAAwEDBkBoAAAAAwMBCwABAAECAAIDSAwEAkgMAwVIDAYESAwFBkgMFAEAAAAFAgMFBgQXBAAAAAAAAAAW", + 210s - "smiles": "COc1cc[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEB0A4AAAAAwEDBkBoAAAAAwMBB2AoAAAAAwMGQGgAAAADAwELAAEAAQIgAgNoDAQCaAwDBWgMBgRoDAUGaAwUAQAAAAUCAwUGBBcEAAAAAAAAABY=", + 210s - "smiles": "COc1ccn[nH]1" + 210s - } + 210s - ], + 210s - "template": { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBoAAAAAAEDCAAoAAAAAAIGQCgAAAAABAcQKAAAAAACGQ0AAABBdG9tQXRvbWljTnVtIRoHAAAAAAAAABwAKwZAaAAAAAMDAQcQKAAAAAACGQ0AAABBdG9tQXRvbWljTnVtIRoHAAAAAAAAABwAKwZAaAAAAAMDAQsAAQABAgACAxgAGRwAAABTaW5nbGVPckRvdWJsZU9yQXJvbWF0aWNCb25kIRoBAAAAAAAAABwAKwQCGAAZHAAAAFNpbmdsZU9yRG91YmxlT3JBcm9tYXRpY0JvbmQhGgEAAAAAAAAAHAArAwVIDAYEGAAZHAAAAFNpbmdsZU9yRG91YmxlT3JBcm9tYXRpY0JvbmQhGgEAAAAAAAAAHAArBQYYABkcAAAAU2luZ2xlT3JEb3VibGVPckFyb21hdGljQm9uZCEaAQAAAAAAAAAcACsXBAAAAAAAAAAW", + 210s - "smarts": "[#6]-[#8]-[#6]1-,=,:[#7]:[#7]-,=,:[#6]-,=,:[#6]-,=,:1" + 210s - }, + 210s - "modifiedAtoms": [ + 210s - "3", + 210s - "5" + 210s - ], + 210s - "modifiedBonds": [ + 210s - "2", + 210s - "3", + 210s - "5", + 210s - "6" + 210s - ] + 210s - }, + 210s - { + 210s - "tautomers": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAIAAAACAAAAIABBgBoAAAAAAEDCAAoAAAAAAIIACgAAAAAAgZAKAAAAAAEB0AoAAAAAwMGQGgAAAADAwEHQDgAAAADAQMGQGgAAAADAwELAAEAAQIAAgMAAwRIDAUDSAwEBkgMBwVIDAYHSAwUAQAAAAUDBAYHBRcEAAAAAAAAABY=", + 210s - "smiles": "COOc1cc[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAIAAAACAAAAIABBgBgAAAAAQMIACAAAAACCAAoAAAAAwIGQCgAAAADBAdAOAAAAAMBAwZAaAAAAAMDAQdgKAAAAAMDBkBoAAAAAwMBCwABAAECAAIDIAMEaAwFA2gMBAZoDAcFaAwGB2gMFAEAAAAFAwQGBwUXBAAAAAAAAAAW", + 210s - "smiles": "COOc1ccn[nH]1" + 210s - } + 210s - ], + 210s - "template": { + 210s - "pkl": "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", + 210s - "smarts": "[#6]-[#8]-[#8]-[#6]1-,=,:[#7]:[#7]-,=,:[#6]-,=,:[#6]-,=,:1" + 210s - }, + 210s - "modifiedAtoms": [ + 210s - "4", + 210s - "6" + 210s - ], + 210s - "modifiedBonds": [ + 210s - "3", + 210s - "4", + 210s - "6", + 210s - "7" + 210s - ] + 210s - }, + 210s - { + 210s - "tautomers": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAJAAAACQAAAIABBgBoAAAAAAEDCAAoAAAAAAIIACgAAAAAAggAKAAAAAACBkAoAAAAAAQHQCgAAAADAwZAaAAAAAMDAQdAOAAAAAMBAwZAaAAAAAMDAQsAAQABAgACAwADBAAEBUgMBgRIDAUHSAwIBkgMBwhIDBQBAAAABQQFBwgGFwQAAAAAAAAAFg==", + 210s - "smiles": "COOOc1cc[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAJAAAACQAAAIABBgBgAAAAAQMIACAAAAACCAAgAAAAAggAKAAAAAMCBkAoAAAAAwQHQDgAAAADAQMGQGgAAAADAwEHYCgAAAADAwZAaAAAAAMDAQsAAQABAgACAwADBCAEBWgMBgRoDAUHaAwIBmgMBwhoDBQBAAAABQQFBwgGFwQAAAAAAAAAFg==", + 210s - "smiles": "COOOc1ccn[nH]1" + 210s - } + 210s - ], + 210s - "template": { + 210s - "pkl": "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",+ 210s - "smarts": "[#6]-[#8]-[#8]-[#8]-[#6]1-,=,:[#7]:[#7]-,=,:[#6]-,=,:[#6]-,=,:1" + 210s - }, + 210s - "modifiedAtoms": [ + 210s - "5", + 210s - "7" + 210s - ], + 210s - "modifiedBonds": [ + 210s - "4", + 210s - "5", + 210s - "7", + 210s - "8" + 210s - ] + 210s - } + 210s - ] + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s + ^ 210s select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, false); 210s - mol_to_xqmol 210s ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "3", + 210s - "tautomers": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEB0AoAAAAAwMHQDgAAAADAQMGQGgAAAADAwEGQGgAAAADAwELAAEAAQIgAgNoDAMEaAwEBWgMBQZoDAYCaAwUAQAAAAUCAwQFBhcEAAAAAAAAABY=", + 210s - "smiles": "COc1cc[nH]n1 |LN:1:1.3|" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEB0A4AAAAAwEDB2AoAAAAAwMGQGgAAAADAwEGQGgAAAADAwELAAEAAQIgAgNoDAMEaAwEBWgMBQZoDAYCaAwUAQAAAAUCAwQFBhcEAAAAAAAAABY=", + 210s - "smiles": "COc1ccn[nH]1 |LN:1:1.3|" + 210s - } + 210s - ], + 210s - "template": { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEBxAoAAAAAAIZDQAAAEF0b21BdG9taWNOdW0hGgcAAAAAAAAAHAArBxAoAAAAAAIZDQAAAEF0b21BdG9taWNOdW0hGgcAAAAAAAAAHAArBkBoAAAAAwMBBkBoAAAAAwMBCwABAAECIAIDGAAZHAAAAFNpbmdsZU9yRG91YmxlT3JBcm9tYXRpY0JvbmQhGgEAAAAAAAAAHAArAwRoDAQFGAAZHAAAAFNpbmdsZU9yRG91YmxlT3JBcm9tYXRpY0JvbmQhGgEAAAAAAAAAHAArBQYYABkcAAAAU2luZ2xlT3JEb3VibGVPckFyb21hdGljQm9uZCEaAQAAAAAAAAAcACsGAhgAGRwAAABTaW5nbGVPckRvdWJsZU9yQXJvbWF0aWNCb25kIRoBAAAAAAAAABwAKxQBAAAABQIDBAUGFwQAAAAAAAAAFg==",+ 210s - "smarts": "[#6]-[#8]-[#6]1-,=,:[#7]:[#7]-,=,:[#6]-,=,:[#6]-,=,:1 |LN:1:1.3|" + 210s - }, + 210s - "modifiedAtoms": [ + 210s - "3", + 210s - "4" + 210s - ], + 210s - "modifiedBonds": [ + 210s - "2", + 210s - "4", + 210s - "5", + 210s - "6" + 210s - ] + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, false); 210s + ^ 210s select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, true, false); 210s - mol_to_xqmol 210s --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "2", + 210s - "mols": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBoAAAAAAEDCAAoAAAAAAIGQCgAAAAABAdAKAAAAAMDBkBoAAAAAwMBB0A4AAAAAwEDBkBoAAAAAwMBCwABAAECAAIDSAwEAkgMAwVIDAYESAwFBkgMFwQAAAAAAAAAFg==", + 210s - "smiles": "COc1cc[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAIAAAACAAAAIABBgBoAAAAAAEDCAAoAAAAAAIIACgAAAAAAgZAKAAAAAAEB0AoAAAAAwMGQGgAAAADAwEHQDgAAAADAQMGQGgAAAADAwELAAEAAQIAAgMAAwRIDAUDSAwEBkgMBwVIDAYHSAwXBAAAAAAAAAAW", + 210s - "smiles": "COOc1cc[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAJAAAACQAAAIABBgBoAAAAAAEDCAAoAAAAAAIIACgAAAAAAggAKAAAAAACBkAoAAAAAAQHQCgAAAADAwZAaAAAAAMDAQdAOAAAAAMBAwZAaAAAAAMDAQsAAQABAgACAwADBAAEBUgMBgRIDAUHSAwIBkgMBwhIDBcEAAAAAAAAABY=",+ 210s - "smiles": "COOOc1cc[nH]n1" + 210s - } + 210s - ] + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, true, fal... 210s + ^ 210s select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, false, false); 210s - mol_to_xqmol 210s ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "1", + 210s - "mol": { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEB0AoAAAAAwMHQDgAAAADAQMGQGgAAAADAwEGQGgAAAADAwELAAEAAQIgAgNoDAMEaAwEBWgMBQZoDAYCaAwUAQAAAAUCAwQFBhcEAAAAAAAAABY=",+ 210s - "smiles": "COc1cc[nH]n1" + 210s - } + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, false, fa... 210s + ^ 210s select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, false, false, true); 210s - mol_to_xqmol 210s ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "1", + 210s - "mol": { + 210s - "pkl": "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",+ 210s - "smarts": "[#6]-[#8]-[#6&D3]1:[#7&D2]:[#7&D2]:[#6&D2]:[#6&D2]:1" + 210s - } + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol, false, fa... 210s + ^ 210s -- substructure searching 210s select 'Cc1[nH]nc(F)c1'::mol @> mol_to_xqmol('Cc1n[nH]c(F)c1'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'Cc1[nH]nc(F)c1'::mol @> mol_to_xqmol('Cc1n[nH]c(F)c1... 210s + ^ 210s select substruct('Cc1[nH]nc(F)c1'::mol,mol_to_xqmol('Cc1n[nH]c(F)c1'::mol)); 210s - substruct 210s ------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('Cc1[nH]nc(F)c1'::mol,mol_to_xqmol('Cc1n[nH... 210s + ^ 210s select substruct('Cc1[nH]nc(F)c1'::mol,mol_to_xqmol('Cc1n[nH]c(F)n1'::mol)); 210s - substruct 210s ------------ 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('Cc1[nH]nc(F)c1'::mol,mol_to_xqmol('Cc1n[nH... 210s + ^ 210s select substruct('COC'::mol,'COC |LN:1:1.3|'::mol); 210s - substruct 210s ------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('COC'::mol,'COC |LN:1:1.3|'::mol); 210s + ^ 210s select substruct('COC'::mol,mol_to_xqmol('COC |LN:1:1.3|'::mol)); 210s - substruct 210s ------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('COC'::mol,mol_to_xqmol('COC |LN:1:1.3|'::m... 210s + ^ 210s select substruct('COOC'::mol,'COC |LN:1:1.3|'::mol); 210s - substruct 210s ------------ 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('COOC'::mol,'COC |LN:1:1.3|'::mol); 210s + ^ 210s select substruct('COOC'::mol,mol_to_xqmol('COC |LN:1:1.3|'::mol)); 210s - substruct 210s ------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('COOC'::mol,mol_to_xqmol('COC |LN:1:1.3|'::... 210s + ^ 210s select substruct('COOOC'::mol,mol_to_xqmol('COC |LN:1:1.3|'::mol)); 210s - substruct 210s ------------ 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('COOOC'::mol,mol_to_xqmol('COC |LN:1:1.3|':... 210s + ^ 210s select substruct('COOOOC'::mol,mol_to_xqmol('COC |LN:1:1.3|'::mol)); 210s - substruct 210s ------------ 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select substruct('COOOOC'::mol,mol_to_xqmol('COC |LN:1:1.3|'... 210s + ^ 210s select 'COc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...'COc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s + ^ 210s select 'COc1[n][nH]cc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...Oc1[n][nH]cc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s + ^ 210s select 'COOc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...COOc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s + ^ 210s select 'COOOc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...OOOc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s + ^ 210s select 'COOOOc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...OOOc1[nH]ncc1'@>mol_to_xqmol('COC1=NNC=C1 |LN:1:1.3|'::mol); 210s + ^ 210s -- edge cases and error handling 210s select mol_to_xqmol('C1'::mol); 210s -ERROR: could not create molecule from SMILES 'C1' 210s +ERROR: type "mol" does not exist 210s LINE 1: select mol_to_xqmol('C1'::mol); 210s - ^ 210s + ^ 210s select mol_to_xqmol('c1cc1'::mol); 210s -ERROR: MolToXQMol: Can't kekulize mol. Unkekulized atoms: 0 1 2 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('c1cc1'::mol); 210s + ^ 210s select mol_to_xqmol('COC1=NNC=C1'::mol); 210s - mol_to_xqmol 210s ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 210s - { dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 210s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation) 210s + 210s - "xqm_type": "3", + 210s - "tautomers": [ + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEB0AoAAAAAwMHQDgAAAADAQMGQGgAAAADAwEGQGgAAAADAwELAAEAAQIgAgNoDAMEaAwEBWgMBQZoDAYCaAwUAQAAAAUCAwQFBhcEAAAAAAAAABY=", + 210s - "smiles": "COc1cc[nH]n1" + 210s - }, + 210s - { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAHAAAABwAAAIABBgBgAAAAAQMIACgAAAADAgZAKAAAAAMEB0A4AAAAAwEDB2AoAAAAAwMGQGgAAAADAwEGQGgAAAADAwELAAEAAQIgAgNoDAMEaAwEBWgMBQZoDAYCaAwUAQAAAAUCAwQFBhcEAAAAAAAAABY=", + 210s - "smiles": "COc1ccn[nH]1" + 210s - } + 210s - ], + 210s - "template": { + 210s - "pkl": "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",+ 210s - "smarts": "[#6]-[#8]-[#6]1-,=,:[#7]:[#7]-,=,:[#6]-,=,:[#6]-,=,:1" + 210s - }, + 210s - "modifiedAtoms": [ + 210s - "3", + 210s - "4" + 210s - ], + 210s - "modifiedBonds": [ + 210s - "2", + 210s - "4", + 210s - "5", + 210s - "6" + 210s - ] + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('COC1=NNC=C1'::mol); 210s + ^ 210s select 'CCOC1=NNC=C1'::mol@>mol_to_xqmol('COC1=NNC=C1'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CCOC1=NNC=C1'::mol@>mol_to_xqmol('COC1=NNC=C1'::mol)... 210s + ^ 210s select mol_to_xqmol('CCCC'::mol); 210s - mol_to_xqmol 210s ----------------------------------------------------------------------------------------------------------------------------------------- 210s - { + 210s - "xqm_type": "1", + 210s - "mol": { + 210s - "pkl": "776t3gAAAAAPAAAAAAAAAAAAAAAEAAAAAwAAAIABBgBgAAAAAQMGAGAAAAACAgYAYAAAAAICBgBgAAAAAQMLAAEAAQIAAgMAFAAAAAAXBAAAAAAAAAAW",+ 210s - "smiles": "CCCC" + 210s - } + 210s - } + 210s - 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select mol_to_xqmol('CCCC'::mol); 210s + ^ 210s select 'CCCCOC'::mol@>mol_to_xqmol('CCCC'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'CCCCOC'::mol@>mol_to_xqmol('CCCC'::mol); 210s + ^ 210s -- interaction with the generic groups 210s select 'COC1=NNC(CC)=C1'::mol @>> mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}'); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COC1=NNC(CC)=C1'::mol @>> mol_adjust_query_propertie... 210s + ^ 210s select 'COC1=NNC(C=C)=C1'::mol @>> mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}'); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COC1=NNC(C=C)=C1'::mol @>> mol_adjust_query_properti... 210s + ^ 210s select 'COC1=NNC(CC)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COC1=NNC(CC)=C1'::mol @>> mol_to_xqmol(mol_adjust_qu... 210s + ^ 210s select 'COC1=NNC(C=C)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COC1=NNC(C=C)=C1'::mol @>> mol_to_xqmol(mol_adjust_q... 210s + ^ 210s select 'COOC1=NNC(CC)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COOC1=NNC(CC)=C1'::mol @>> mol_to_xqmol(mol_adjust_q... 210s + ^ 210s select 'COOC1=NNC(C=C)=C1'::mol @>> mol_to_xqmol(mol_adjust_query_properties('COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|'::mol, 210s '{"makeDummiesQueries":true, "setGenericQueryFromProperties": true}')); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'COOC1=NNC(C=C)=C1'::mol @>> mol_to_xqmol(mol_adjust_... 210s + ^ 210s -- problems we've encountered 210s select 'CCOC(=O)c1cc2n(n1)C(C(=O)O)Nc1cc(Cl)ccc1-2'::mol @> mol_to_xqmol('COCc1n[nH]c(C)c1 |LN:1:1.3|'::mol); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: ...ect 'CCOC(=O)c1cc2n(n1)C(C(=O)O)Nc1cc(Cl)ccc1-2'::mol @> mol... 210s + ^ 210s -- link nodes and variable attachment points 210s select 'Cc1ccnc2nc(CN)[nH]c12'::mol@>>mol_to_xqmol(mol_from_ctab('qry 210s Mrv2305 09052314502D 210s @@ -466,11 +184,9 @@ 210s M V30 END BOND 210s M V30 END CTAB 210s M END')); 210s - ?column? 210s ----------- 210s - t 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'Cc1ccnc2nc(CN)[nH]c12'::mol@>>mol_to_xqmol(mol_from_... 210s + ^ 210s select 'c1ccnc2nc(CN)[nH]c12'::mol@>>mol_to_xqmol(mol_from_ctab('qry 210s Mrv2305 09052314502D 210s 210s @@ -509,8 +225,6 @@ 210s M V30 END BOND 210s M V30 END CTAB 210s M END')); 210s - ?column? 210s ----------- 210s - f 210s -(1 row) 210s - 210s +ERROR: type "mol" does not exist 210s +LINE 1: select 'c1ccnc2nc(CN)[nH]c12'::mol@>>mol_to_xqmol(mol_from_c... 210s + ^ 210s ### End 17 installcheck (FAILED with exit code 1) ### 211s autopkgtest [20:44:13]: test installcheck: -----------------------] 211s installcheck FAIL non-zero exit status 1 211s autopkgtest [20:44:13]: test installcheck: - - - - - - - - - - results - - - - - - - - - - 212s autopkgtest [20:44:14]: @@@@@@@@@@@@@@@@@@@@ summary 212s installcheck FAIL non-zero exit status 1 224s nova [W] Skipping flock in bos03-arm64 224s Creating nova instance adt-plucky-arm64-rdkit-20241123-204041-juju-7f2275-prod-proposed-migration-environment-15-997c453a-f89c-4751-89d9-2268365f540a from image adt/ubuntu-plucky-arm64-server-20241119.img (UUID 254dc414-4366-404b-b85c-a4e26b3194ad)...