[Debichem-devel] Bug#1072693: smiles-scripts: FTBFS (test failures) with newer libxml2 (or libxml-libxml-perl)
gregor herrmann
gregoa at debian.org
Thu Jun 6 17:01:25 BST 2024
Source: smiles-scripts
Version: 0.2.0+dfsg1-5
Severity: serious
Tags: ftbfs sid trixie
Justification: fails to build from source
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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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