Your message dated Mon, 09 Jan 2023 09:08:12 +0000
with message-id <[email protected]>
and subject line Bug#1026325: fixed in smiles-scripts 0.2.0+dfsg1-2
has caused the Debian Bug report #1026325,
regarding libchemistry-opensmiles-perl breaks smiles-scripts autopkgtest:
output changed
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1026325: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1026325
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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: [email protected]
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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: smiles-scripts
Source-Version: 0.2.0+dfsg1-2
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
smiles-scripts, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated smiles-scripts package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 09 Jan 2023 03:30:24 -0500
Source: smiles-scripts
Architecture: source
Version: 0.2.0+dfsg1-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1026325
Changes:
smiles-scripts (0.2.0+dfsg1-2) unstable; urgency=medium
.
* Adjust to changes in Chemistry::OpenSMILES v0.8.4 (Closes: #1026325)
* Tests depend on liblog4j1.2-java.
* Bump copyright years.
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