Your message dated Tue, 02 Jul 2024 08:41:03 +0000
with message-id <[email protected]>
and subject line Bug#1072693: fixed in smiles-scripts 0.2.0+dfsg1-6
has caused the Debian Bug report #1072693,
regarding smiles-scripts: FTBFS (test failures) with newer libxml2 (or
libxml-libxml-perl)
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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immediately.)
--
1072693: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1072693
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: smiles-scripts
Version: 0.2.0+dfsg1-5
Severity: serious
Tags: ftbfs sid trixie
Justification: fails to build from source
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
On libxml-libxml-perl's tracker page I noticed that autopkgtest
failures in smiles-scripts and had a look at the package. And it
currently doesn't build, as the tests fail here as well:
#v+
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/smiles-scripts-0.2.0+dfsg1'
rm tests/cases/cdkcif2smiles_002.*
rm tests/cases/cdkcif2smiles_003.*
rm tests/cases/cdkcif2xyz_002.*
rm tests/cases/cdkcif2xyz_003.*
rm tests/cases/cdkdepict_001.*
rm tests/cases/cdkdepict_004.*
rm tests/cases/cdkdepict_005.*
rm tests/cases/cdkdepict_006.*
rm tests/cases/cdkdepict_008.*
rm tests/cases/cdkdepict_009.*
rm tests/cases/cdkdepict_010.*
rm tests/cases/cdkdepict_022.*
rm tests/cases/cdkdepict_023.*
rm tests/cases/cdkdepict-cgi_001.*
rm tests/cases/cdksdf2smiles_005.*
rm tests/cases/cdksdf2smiles_007.*
rm tests/cases/cdksdf2smiles_009.*
rm tests/cases/cdksdf2smiles_010.*
rm tests/cases/sdf-to-smi_002.*
dh_auto_test -- MODULE_BUILD_PARSE_YAPP= CHEMISTRY_OPENSMILES=
make -j4 test MODULE_BUILD_PARSE_YAPP= CHEMISTRY_OPENSMILES=
make[2]: Entering directory '/build/smiles-scripts-0.2.0+dfsg1'
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
find: 'externals': No such file or directory
find: 'externals': No such file or directory
tests/cases/cdkcif2smiles_001.opt:
tests/cases/cdkcif2xyz_001.opt:
tests/cases/cdkdepict-cgi_002.sh:
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
FAILED:
tests/cases/cdkrecharge_002.sh: 1c1
< cdkdepict: tests/cases/cdkdepict_007.inp(1): ERROR,
org.openscience.cdk.exception.InvalidSmilesException: could not parse
'n1cccc1', a valid kekulé structure could not be assigned
- ---
> cdkdepict: tests/cases/cdkdepict_007.inp(1): ERROR,
> org.openscience.cdk.exception.InvalidSmilesException: could not parse
> 'n1cccc1', a valid kekul? structure could not be assigned
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
OK
tests/cases/cdkrecharge_008.inp: OK
tests/cases/cdkrecharge_009.opt:
tests/cases/cdkrecharge_010.opt: OK
tests/cases/cdkrecharge_011.opt: OK
OK
tests/cases/cdkrecharge_012.inp:
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
OK
tests/cases/cdkrecharge_020.inp:
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: FAILED:
10,12d9
< tests/cases/cml-to-smi_005.inp:2: parser error : Extra content at the end of
the document
< g/schema"
id="id/opt/eprints3/archives/ecrystals/documents/disk0/00/00/07/15/01/
<
^
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_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: FAILED:
2350c2350
< cdkrecharge: tests/cases/cdkrecharge_015.inp(2350) 4303782: ERROR,
org.openscience.cdk.exception.InvalidSmilesException: could not parse
'[Au]123=c4n(CC5N([Cu]61[Cl][Cu]2([Cl]6)N1C(Cn2c3n(cc2)C)CCC2CCCCC12)C1C(CC5)CCCC1)ccn4C',
a valid kekulé structure could not be assigned
- ---
> cdkrecharge: tests/cases/cdkrecharge_015.inp(2350) 4303782: ERROR,
> org.openscience.cdk.exception.InvalidSmilesException: could not parse
> '[Au]123=c4n(CC5N([Cu]61[Cl][Cu]2([Cl]6)N1C(Cn2c3n(cc2)C)CCC2CCCCC12)C1C(CC5)CCCC1)ccn4C',
> a valid kekul? structure could not be assigned
3486c3486
< cdkrecharge: tests/cases/cdkrecharge_015.inp(3486) 7010535: ERROR,
org.openscience.cdk.exception.InvalidSmilesException: could not parse
'[Bi]1(Cl)(Cl)(Cl)([O]=P(c2c(P(=[O]1)(c1ccccc1)c1ccccc1)cccc2)(c1ccccc1)c1ccccc1)o1cccc1',
a valid kekulé structure could not be assigned
- ---
> cdkrecharge: tests/cases/cdkrecharge_015.inp(3486) 7010535: ERROR,
> org.openscience.cdk.exception.InvalidSmilesException: could not parse
> '[Bi]1(Cl)(Cl)(Cl)([O]=P(c2c(P(=[O]1)(c1ccccc1)c1ccccc1)cccc2)(c1ccccc1)c1ccccc1)o1cccc1',
> a valid kekul? structure could not be assigned
3633c3633
< cdkrecharge: tests/cases/cdkrecharge_015.inp(3633) 7016625: ERROR,
org.openscience.cdk.exception.InvalidSmilesException: could not parse
'[Cd]1234(N5CCCCC5C5N1N(CC5)Cc1ccc(CN5N2C(C2N3CCCC2)CC5)o41)[F][B](F)(F)F', a
valid kekulé structure could not be assigned
- ---
> cdkrecharge: tests/cases/cdkrecharge_015.inp(3633) 7016625: ERROR,
> org.openscience.cdk.exception.InvalidSmilesException: could not parse
> '[Cd]1234(N5CCCCC5C5N1N(CC5)Cc1ccc(CN5N2C(C2N3CCCC2)CC5)o41)[F][B](F)(F)F', a
> valid kekul? structure could not be assigned
3870c3870
< cdkrecharge: tests/cases/cdkrecharge_015.inp(3870) 7026929: ERROR,
org.openscience.cdk.exception.InvalidSmilesException: could not parse
'[Cu]1234[N]56CC[NH]1CC[N]2(CC[NH]3CC5)Cc1c2o4c3c(C6)cccc3c2ccc1', a valid
kekulé structure could not be assigned
- ---
> cdkrecharge: tests/cases/cdkrecharge_015.inp(3870) 7026929: ERROR,
> org.openscience.cdk.exception.InvalidSmilesException: could not parse
> '[Cu]1234[N]56CC[NH]1CC[N]2(CC[NH]3CC5)Cc1c2o4c3c(C6)cccc3c2ccc1', a valid
> kekul? structure could not be assigned
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
OK
tests/cases/smi_isomorphism_007.sh:
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: OK
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: OK
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
OK
OK
OK
make[2]: Leaving directory '/build/smiles-scripts-0.2.0+dfsg1'
find tests/outputs -name '*.diff' -a -size +0 | xargs --no-run-if-empty -i echo
FAILED: {}
FAILED: tests/outputs/cdkdepict_007.diff
FAILED: tests/outputs/cdkrecharge_015.diff
FAILED: tests/outputs/cml-to-smi_005.diff
find tests/outputs -name '*.diff' -a -size +0 | xargs --no-run-if-empty false #
Detect test failures
make[1]: *** [debian/rules:35: override_dh_auto_test] Error 123
#v-
Cheers,
gregor
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--- End Message ---
--- Begin Message ---
Source: smiles-scripts
Source-Version: 0.2.0+dfsg1-6
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: Tue, 02 Jul 2024 04:16:35 -0400
Source: smiles-scripts
Architecture: source
Version: 0.2.0+dfsg1-6
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1072693
Changes:
smiles-scripts (0.2.0+dfsg1-6) unstable; urgency=medium
.
* Ignore incompatible tests (Closes: #1072693)
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