Source: rdkit Version: 202103.5-1 X-Debbugs-CC: debian-ci@lists.debian.org Severity: serious User: debian-ci@lists.debian.org Usertags: regression Dear maintainer(s),With a recent upload of rdkit the autopkgtest of rdkit fails in testing when that autopkgtest is run with the binary packages of rdkit from unstable. It passes when run with only packages from testing. In tabular form:
pass fail
rdkit from testing 202103.5-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?
More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=rdkit https://ci.debian.net/data/autopkgtest/testing/amd64/r/rdkit/16957749/log.gz ### PostgreSQL 14 installcheck ### Creating new PostgreSQL cluster 14/regress ...make: Entering directory '/tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit' /usr/lib/postgresql/14/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=/tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src --bindir='/usr/lib/postgresql/14/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 bfpgin sfpgist slfpgist fps reaction (using postmaster on localhost, port 5433)
============== dropping database "contrib_regression" ============== NOTICE: database "contrib_regression" does not exist, skipping DROP DATABASE ============== creating database "contrib_regression" ============== CREATE DATABASE ALTER DATABASE ============== running regression test queries ============== test rdkit-91 ... ok 2975 ms test props ... ok 69 ms test btree ... ok 536 ms test molgist ... ok 1352 ms test bfpgist-91 ... ok 97 ms test bfpgin ... ok 221 ms test sfpgist ... ok 80 ms test slfpgist ... ok 96 ms test fps ... ok 88 ms test reaction ... FAILED 3389 ms ======================= 1 of 10 tests failed. ======================= The differences that caused some tests to fail can be viewed in thefile "/tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/regression.diffs". A copy of the test summary that you see above is saved in the file "/tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/regression.out".
make: *** [/usr/lib/postgresql/14/lib/pgxs/src/makefiles/pgxs.mk:433: installcheck] Error 1 make: Leaving directory '/tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit' *** /tmp/pg_virtualenv.TNKdYW/log/postgresql-14-regress.log (last 100 lines) *** 2021-11-24 12:12:29.980 UTC [4556] LOG: starting PostgreSQL 14.1 (Debian 14.1-1) on x86_64-pc-linux-gnu, compiled by gcc (Debian 11.2.0-10) 11.2.0, 64-bit 2021-11-24 12:12:29.980 UTC [4556] LOG: listening on IPv6 address "::1", port 5433 2021-11-24 12:12:29.980 UTC [4556] LOG: listening on IPv4 address "127.0.0.1", port 5433 2021-11-24 12:12:29.980 UTC [4556] LOG: listening on Unix socket "/tmp/.s.PGSQL.5433" 2021-11-24 12:12:29.982 UTC [4557] LOG: database system was shut down at 2021-11-24 12:12:29 UTC 2021-11-24 12:12:29.985 UTC [4556] LOG: database system is ready to accept connections 2021-11-24 12:12:32.321 UTC [4621] debci@contrib_regression WARNING: could not create molecule from SMILES 'c1ccccc' 2021-11-24 12:12:32.321 UTC [4621] debci@contrib_regression WARNING: could not create molecule from SMILES 'cccccc' 2021-11-24 12:12:32.323 UTC [4621] debci@contrib_regression WARNING: could not create molecule from SMILES 'c1ccc' 2021-11-24 12:12:35.211 UTC [4621] debci@contrib_regression ERROR: Unknown flag value: 'BOGUS'. Flags ignored. 2021-11-24 12:12:35.211 UTC [4621] debci@contrib_regression STATEMENT: select 'C1C(C)C1CCCC'::mol @> mol_adjust_query_properties('C1CC1CC'::mol,'{"adjustDegreeFlags":"bogus"}'); 2021-11-24 12:12:35.214 UTC [4621] debci@contrib_regression WARNING: could not create molecule from CTAB 'a' 2021-11-24 12:12:35.214 UTC [4621] debci@contrib_regression WARNING: could not create molecule from SMILES 'a' 2021-11-24 12:12:35.214 UTC [4621] debci@contrib_regression WARNING: could not create molecule from SMILES 'C1C' 2021-11-24 12:12:35.285 UTC [4625] debci@contrib_regression WARNING: computeNMMolHash: hash BogusValue not recognized, using AnonymousGraph
Dropping cluster 14/regress ...**** /tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/regression.diffs **** diff -U3 /tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/expected/reaction.out /tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/results/reaction.out --- /tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/expected/reaction.out 2021-11-24 12:11:43.000000000 +0000 +++ /tmp/autopkgtest-lxc.d5zz2gpa/downtmp/build.YIU/src/Code/PgSQL/rdkit/results/reaction.out 2021-11-24 12:12:41.157050919 +0000
@@ -20,15 +20,15 @@ (1 row)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]'); - reaction_from_smarts
----------------------------------------------------------------------------------- c([cH:4][cH:3][cH:2][cH2:1])[cH2:5]>CC(=O)O>n([cH:4][cH:3][cH:2][cH2:1])[cH2:5] + reaction_from_smarts +-------------------------------------------------------------------
+ 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] (1 row)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]'); - reaction_from_smarts
------------------------------------------------------------------------------------------ c([cH:4][cH:3][cH:2][cH2:1])[cH2:5]>CC(=O)O.FC(F)F>n([cH:4][cH:3][cH:2][cH2:1])[cH2:5] + reaction_from_smarts
+--------------------------------------------------------------------------
+ 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]
(1 row)
SELECT reaction_from_smarts('c1ccc[n,c]c1>>c1nccnc1');
### End 14 installcheck (FAILED with exit code 1) ###
autopkgtest [12:12:41]: test installcheck
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