[Debichem-devel] Bug#1000579: rdkit: autopkgtest regression

Paul Gevers elbrus at debian.org
Thu Nov 25 10:27:21 GMT 2021


Source: rdkit
Version: 202103.5-1
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at 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 the
file 
"/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 at contrib_regression WARNING: 
could not create molecule from SMILES 'c1ccccc'
2021-11-24 12:12:32.321 UTC [4621] debci at contrib_regression WARNING: 
could not create molecule from SMILES 'cccccc'
2021-11-24 12:12:32.323 UTC [4621] debci at contrib_regression WARNING: 
could not create molecule from SMILES 'c1ccc'
2021-11-24 12:12:35.211 UTC [4621] debci at contrib_regression ERROR: 
Unknown flag value: 'BOGUS'. Flags ignored.
2021-11-24 12:12:35.211 UTC [4621] debci at 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 at contrib_regression WARNING: 
could not create molecule from CTAB 'a'
2021-11-24 12:12:35.214 UTC [4621] debci at contrib_regression WARNING: 
could not create molecule from SMILES 'a'
2021-11-24 12:12:35.214 UTC [4621] debci at contrib_regression WARNING: 
could not create molecule from SMILES 'C1C'
2021-11-24 12:12:35.285 UTC [4625] debci at 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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