Bug#1026325: libchemistry-opensmiles-perl breaks smiles-scripts autopkgtest: output changed
Paul Gevers
elbrus at debian.org
Sun Dec 18 16:48:53 GMT 2022
Source: libchemistry-opensmiles-perl, smiles-scripts
Control: found -1 libchemistry-opensmiles-perl/0.8.4-1
Control: found -1 smiles-scripts/0.2.0+dfsg1-1
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of libchemistry-opensmiles-perl the autopkgtest of
smiles-scripts fails in testing when that autopkgtest is run with the
binary packages of libchemistry-opensmiles-perl from unstable. It passes
when run with only packages from testing. In tabular form:
pass fail
libchemistry-opensmiles-perl from testing 0.8.4-1
smiles-scripts from testing 0.2.0+dfsg1-1
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 of
libchemistry-opensmiles-perl to testing [1]. Due to the nature of this
issue, I filed this bug report against both packages. Can you please
investigate the situation and reassign the bug to the right package?
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=libchemistry-opensmiles-perl
https://ci.debian.net/data/autopkgtest/testing/amd64/s/smiles-scripts/29465786/log.gz
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
make: svnversion: No such file or directory
find: ‘src/net’: No such file or directory
find: ‘src/net’: No such file or directory
find: ‘src/net’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
mkjavadepend src classes > .depend
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
make: svnversion: No such file or directory
find: ‘src/net’: No such file or directory
find: ‘src/net’: No such file or directory
find: ‘src/net’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
find: ‘externals’: No such file or directory
tests/cases/cdkcif2smiles_001.opt: OK
tests/cases/cdkcif2xyz_001.opt: OK
tests/cases/cdkdepict-cgi_002.sh: OK
tests/cases/cdkdepict_002.inp: OK
tests/cases/cdkdepict_003.opt: OK
tests/cases/cdkdepict_007.inp: OK
tests/cases/cdkdepict_021.opt: OK
tests/cases/cdkrecharge_001.opt: OK
tests/cases/cdkrecharge_002.sh: OK
tests/cases/cdkrecharge_003.opt: OK
tests/cases/cdkrecharge_004.opt: OK
tests/cases/cdkrecharge_005.opt: OK
tests/cases/cdkrecharge_006.inp: OK
tests/cases/cdkrecharge_007.opt: OK
tests/cases/cdkrecharge_008.inp: OK
tests/cases/cdkrecharge_009.opt: OK
tests/cases/cdkrecharge_010.opt: OK
tests/cases/cdkrecharge_011.opt: OK
tests/cases/cdkrecharge_012.inp: OK
tests/cases/cdkrecharge_013.inp: OK
tests/cases/cdkrecharge_014.inp: OK
tests/cases/cdkrecharge_015.inp: OK
tests/cases/cdkrecharge_016.sh: OK
tests/cases/cdkrecharge_017.sh: OK
tests/cases/cdkrecharge_018.inp: OK
tests/cases/cdkrecharge_019.inp: OK
tests/cases/cdkrecharge_020.inp: OK
tests/cases/cdksdf2smiles_001.opt: OK
tests/cases/cdksdf2smiles_002.inp: OK
tests/cases/cdksdf2smiles_003.inp: OK
tests/cases/cdksdf2smiles_004.inp: OK
tests/cases/cdksdf2smiles_006.inp: OK
tests/cases/cdksdf2smiles_008.inp: OK
tests/cases/cml-to-smi_001.inp: OK
tests/cases/cml-to-smi_002.inp: OK
tests/cases/cml-to-smi_003.inp: OK
tests/cases/cml-to-smi_004.inp: OK
tests/cases/cml-to-smi_005.inp: OK
tests/cases/cml-to-smi_006.inp: OK
tests/cases/cml-to-smi_007.inp: OK
tests/cases/cml-to-smi_008.inp: OK
tests/cases/cml-to-smi_009.inp: OK
tests/cases/sdf-to-smi_001.inp: OK
tests/cases/sdf-to-smi_002.inp: OK
tests/cases/sdf-to-smi_003.inp: OK
tests/cases/sdf-to-smi_004.inp: OK
tests/cases/sdf-to-smi_005.inp: OK
tests/cases/sdf-to-smi_006.inp: OK
tests/cases/sdf-to-smi_007.inp: OK
tests/cases/sdf-to-smi_008.inp: OK
tests/cases/sdf-to-smi_009.inp: OK
tests/cases/sdf-to-smi_010.inp: OK
tests/cases/sdf-to-smi_011.inp: OK
tests/cases/sdf-to-smi_012.inp: OK
tests/cases/sdf-to-smi_013.inp: OK
tests/cases/sdf-to-smi_014.inp: OK
tests/cases/sdf-to-smi_015.inp: OK
tests/cases/smi_canonicalise_001.inp: OK
tests/cases/smi_canonicalise_002.inp: OK
tests/cases/smi_canonicalise_003.inp: OK
tests/cases/smi_canonicalise_004.inp: OK
tests/cases/smi_canonicalise_005.inp: OK
tests/cases/smi_canonicalise_006.inp: OK
tests/cases/smi_canonicalise_007.inp: OK
tests/cases/smi_canonicalise_008.inp: OK
tests/cases/smi_canonicalise_009.inp: OK
tests/cases/smi_canonicalise_010.inp: OK
tests/cases/smi_canonicalise_011.inp: OK
tests/cases/smi_canonicalise_012.inp: OK
tests/cases/smi_canonicalise_013.inp: OK
tests/cases/smi_canonicalise_014.inp: OK
tests/cases/smi_canonicalise_015.inp: OK
tests/cases/smi_canonicalise_016.inp: OK
tests/cases/smi_canonicalise_017.inp: OK
tests/cases/smi_canonicalise_018.inp: OK
tests/cases/smi_canonicalise_019.inp: OK
tests/cases/smi_canonicalise_020.inp: OK
tests/cases/smi_canonicalise_021.inp: OK
tests/cases/smi_canonicalise_022.inp: OK
tests/cases/smi_canonicalise_023.inp: OK
tests/cases/smi_canonicalise_024.inp: OK
tests/cases/smi_canonicalise_025.inp: OK
tests/cases/smi_canonicalise_026.inp: OK
tests/cases/smi_canonicalise_027.inp: OK
tests/cases/smi_canonicalise_028.inp: OK
tests/cases/smi_canonicalise_029.inp: OK
tests/cases/smi_isomorphism_001.sh: OK
tests/cases/smi_isomorphism_002.sh: OK
tests/cases/smi_isomorphism_003.sh: OK
tests/cases/smi_isomorphism_004.sh: OK
tests/cases/smi_isomorphism_005.sh: OK
tests/cases/smi_isomorphism_006.sh: OK
tests/cases/smi_isomorphism_007.sh: OK
tests/cases/smi_isomorphism_008.sh: OK
tests/cases/smi_isomorphism_009.sh: OK
tests/cases/smi_isomorphism_010.sh: OK
tests/cases/smi_isomorphism_011.sh: OK
tests/cases/smi_isomorphism_012.sh: OK
tests/cases/smi_isomorphism_013.sh: OK
tests/cases/smi_isomorphism_014.sh: OK
tests/cases/smi_isomorphism_015.sh: OK
tests/cases/smi_isomorphism_016.sh: OK
tests/cases/smi_isomorphism_017.sh: FAILED:
1,12d0
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 33 and 34 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 11 and 47 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 19 and 20 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 33 and 34 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 11 and 47 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 19 and 20 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 11 and 47 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 33 and 34 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 19 and 20 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 11 and 47 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 33 and 34 as there are no eligible single bonds nearby
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 19 and 20 as there are no eligible single bonds nearby
tests/cases/smi_isomorphism_018.sh: OK
tests/cases/smi_isomorphism_019.sh: OK
tests/cases/smi_isomorphism_020.sh: OK
tests/cases/smi_isomorphism_021.sh: OK
tests/cases/smi_isomorphism_022.sh: OK
tests/cases/smi_isomorphism_023.sh: OK
tests/cases/smi_isomorphism_024.sh: OK
tests/cases/smi_isomorphism_025.sh: OK
tests/cases/smi_isomorphism_026.sh: OK
tests/cases/smi_isomorphism_027.sh: OK
tests/cases/smi_isomorphism_028.sh: OK
tests/cases/smi_isomorphism_029.sh: OK
tests/cases/smi_isomorphism_030.sh: OK
tests/cases/smi_isomorphism_031.sh: FAILED:
1d0
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 3 and 4 as there are no eligible single bonds nearby
3d1
< scripts/smi_isomorphism: -(1) XXXXXXX: cannot represent cis/trans bond
between atoms 3 and 4 as there are no eligible single bonds nearby
tests/cases/smi_isomorphism_032.sh: OK
tests/cases/smi_isomorphism_033.sh: OK
tests/cases/smi_isomorphism_034.sh: OK
tests/cases/smi_parse_001.inp: OK
tests/cases/smi_parse_002.inp: OK
tests/cases/smi_parse_003.sh: OK
FAILED: tests/outputs/smi_isomorphism_017.diff
FAILED: tests/outputs/smi_isomorphism_031.diff
autopkgtest [09:23:51]: test upstream
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