[Debichem-devel] Bug#1088896: smiles-scripts: FTBFS: scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties [...], 1 vs. 2
Santiago Vila
sanvila at debian.org
Mon Dec 2 16:48:51 GMT 2024
Package: src:smiles-scripts
Version: 0.2.0+dfsg1-6
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir jars
grep '^ ' MANIFEST.txt | sed 's/[\r ]//g' | xargs -i ln -s {} jars
dh_auto_build -- MODULE_BUILD_PARSE_YAPP= CHEMISTRY_OPENSMILES=
make -j2 "INSTALL=install --strip-program=true" MODULE_BUILD_PARSE_YAPP= CHEMISTRY_OPENSMILES=
make[2]: Entering directory '/<<PKGBUILDDIR>>'
find: ‘externals’: No such file or directory
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sed 's/@VERSION@/0.2.0/' src/Version.java.in \
| sed 's/@VCS_TEXT@//' \
> src/Version.java
mkjavadepend src classes > .depend
find: ‘externals’: No such file or directory
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javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/net/crystallography/vector/space/ChangeOfBasis.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/Version.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/OutputOption.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/net/crystallography/helpers/cdk/OrthogonaliseAtomCoordinates.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/VersionOption.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/EPSOutputOption.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/PDFOutputOption.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/SVGOutputOption.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/CDKCif2SdfHelp.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/CDKCif2SmilesHelp.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/CDKCif2XyzHelp.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/CDKDepictHelp.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/CDKRechargeHelp.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/CDKSdf2SmilesHelp.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/cdkcif2sdf.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/cdkcif2smiles.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/cdkcif2xyz.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/cdkdepict.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/cdkrecharge.java
javac -cp classes:jars/cdk-data.jar:jars/cdk-interfaces.jar:jars/freehep-graphicsio-pdf.jar:jars/cdk-ioformats.jar:jars/cdk-ctab.jar:jars/freehep-graphicsio-ps.jar:jars/vecmath.jar:jars/cdk-sdg.jar:jars/cdk-depict.jar:jars/beam-core.jar:jars/cdk-renderbasic.jar:jars/cdk-render.jar:jars/cdk-isomorphism.jar:jars/cdk-structgen.jar:jars/soptions.jar:jars/log4j-1.2.jar:jars/cdk-io.jar:jars/cdk-smiles.jar:jars/cdk-renderawt.jar:jars/freehep-graphicsio-svg.jar:jars/freehep-graphicsbase.jar:jars/guava.jar:jars/cdk-standard.jar:jars/freehep-graphicsio.jar:jars/cdk-core.jar:jars/freehep-graphics2d.jar:jars/cdk-silent.jar:jars/smiles-scripts-0.2.0.jar -d classes src/cdksdf2smiles.java
jar cfm jars/smiles-scripts-0.2.0.jar MANIFEST.txt -C classes .
ln -sf smiles-scripts-0.2.0.jar jars/smiles-scripts.jar
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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_007.*
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/cdkrecharge_015.*
rm tests/cases/cdksdf2smiles_005.*
rm tests/cases/cdksdf2smiles_007.*
rm tests/cases/cdksdf2smiles_009.*
rm tests/cases/cdksdf2smiles_010.*
rm tests/cases/cml-to-smi_005.*
rm tests/cases/sdf-to-smi_002.*
dh_auto_test -- MODULE_BUILD_PARSE_YAPP= CHEMISTRY_OPENSMILES=
make -j2 test MODULE_BUILD_PARSE_YAPP= CHEMISTRY_OPENSMILES=
make[2]: Entering directory '/<<PKGBUILDDIR>>'
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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: OK
tests/cases/cdkdepict-cgi_002.sh: OK
tests/cases/cdkdepict_002.inp: OK
tests/cases/cdkdepict_003.opt: 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_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: FAILED:
1c1
< C1(=C([N+](:C(:N1([R]))(C([H])([H])([H])))([R]))).[R]
---
> [C]1(=[C]([N+](:C(:[N]1([R]))(C([H])([H])([H])))([R]))).[R]
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: FAILED:
1c1
< C(/C(=C(=C(\C)(/[H]))(\C))(/[H]))
---
> [C](/C(=[C](=C(\[C])(/[H]))(\[C]))(/[H]))
tests/cases/sdf-to-smi_001.inp: OK
tests/cases/sdf-to-smi_003.inp: FAILED:
1c1
< C1(C(O([2H]))(=O([Sr+](O1)(O([2H])([2H])))))(=O).C(=O)([O-])(C(=O)([O-])).C1(C(O([2H]))(=O([Sr+](O1)(O([2H])([2H])))))(=O) 1000002
---
> C1(C(O([2H]))(=[O]([Sr+](O1)([O]([2H])([2H])))))(=O).C(=O)([O-])(C(=O)([O-])).C1(C(O([2H]))(=[O]([Sr+](O1)([O]([2H])([2H])))))(=O) 1000002
tests/cases/sdf-to-smi_004.inp: OK
tests/cases/sdf-to-smi_005.inp: OK
tests/cases/sdf-to-smi_006.inp: FAILED:
1c1
< C1(C(O([2H]))(=O([Sr+](O1)(O([2H])([2H])))))(=O).C(=O)([O-])(C(=O)([O-])).C1(C(O([2H]))(=O([Sr+](O1)(O([2H])([2H])))))(=O) 1000002
---
> C1(C(O([2H]))(=[O]([Sr+](O1)([O]([2H])([2H])))))(=O).C(=O)([O-])(C(=O)([O-])).C1(C(O([2H]))(=[O]([Sr+](O1)([O]([2H])([2H])))))(=O) 1000002
tests/cases/sdf-to-smi_007.inp: FAILED:
1c1
< C1([C@@]2(C([C@@]3(C([C@]1(C([C@@](C2([H])([H]))(C([O-])(=O))(C3([H])([H])))([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H]).[O-](C(=O)([C@]12(C([C@@]3(C([C@](C1([H])([H]))(C([C@](C2([H])([H]))(C3([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H])))).[Cu+2]12(N=3(C(=C(C(=C(C=3([C@](C3(=C(C(=C(C(=N13)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H])))(N=1(C(=C(C(=C(C=1([C@@](C1(=C(C(=C(C(=N21)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H]))) 2203689
---
> C1([C@@]2(C([C@@]3(C([C@]1(C([C@@](C2([H])([H]))(C([O-])(=O))(C3([H])([H])))([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H]).[O-](C(=O)([C@]12(C([C@@]3(C([C@](C1([H])([H]))(C([C@](C2([H])([H]))(C3([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H])))).[Cu+2]12([N]=3(C(=C(C(=C(C=3([C@](C3(=C(C(=C(C(=[N]13)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H])))([N]=1(C(=C(C(=C(C=1([C@@](C1(=C(C(=C(C(=[N]21)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H]))) 2203689
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: FAILED:
1c1
< C1(=C(C(=C(C(=C1)))))([Se](P([Se](C1(=C(C(=C(C(=C1)))))))([Se](C1(=C(C(=C(C(=C1))))))))) 2000618
---
> C1(=[C]([C](=[C]([C](=[C]1)))))([Se](P([Se](C1(=[C]([C](=[C]([C](=[C]1)))))))([Se](C1(=[C]([C](=[C]([C](=[C]1))))))))) 2000618
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: FAILED:
1c1
< C1([C@@]2(C([C@@]3(C([C@]1(C([C@@](C2([H])([H]))(C([O-])(=O))(C3([H])([H])))([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H]).[O-](C(=O)([C@]12(C([C@@]3(C([C@](C1([H])([H]))(C([C@](C2([H])([H]))(C3([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H])))).[Cu+2]12(N=3(C(=C(C(=C(C=3([C@](C3(=C(C(=C(C(=N13)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H])))(N=1(C(=C(C(=C(C=1([C@@](C1(=C(C(=C(C(=N21)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H]))) 2203689
---
> C1([C@@]2(C([C@@]3(C([C@]1(C([C@@](C2([H])([H]))(C([O-])(=O))(C3([H])([H])))([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H]).[O-](C(=O)([C@]12(C([C@@]3(C([C@](C1([H])([H]))(C([C@](C2([H])([H]))(C3([H])([H]))([H]))([H])([H]))([H]))([H])([H]))([H]))([H])([H])))).[Cu+2]12([N]=3(C(=C(C(=C(C=3([C@](C3(=C(C(=C(C(=[N]13)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H])))([N]=1(C(=C(C(=C(C=1([C@@](C1(=C(C(=C(C(=[N]21)([H]))([H]))([H]))([H])))(O([H]))(O([H]))))([H]))([H]))([H]))([H]))) 2203689
tests/cases/smi_canonicalise_002.inp: FAILED:
1c1
< C(n:1(:c(:[n+](C)(:c(:c:1))))) CHEMBL1229272
---
> [C]([n]:1(:[c](:[n+]([C])(:[c](:[c]:1))))) CHEMBL1229272
tests/cases/smi_canonicalise_003.inp: FAILED:
1c1
< C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C(N(C)(C(=O))).C1(C(c:2(:c(:c(:c(:c(:c:2(:c:2(:c1(:c(:c:1(C(C(c:3(:c(:c(:c(:c(:c:3(:c:1(:n:2))))(:c:1(:c(:c:2(:c:3(:c(:c(:c(:c(:n:3([Pt]3(Cl)(n:2(:c(:c:1)(:c:1(:c(:c(:c(:c(:n3:1)))))))))))))))))))))))))(:c:1(:c(:c(C(C)(C)(C))(:c(:c(C(C)(C)(C))(:c:1)))))))))))(:c:1(:c(:c:2(:c:3(:c(:c(:c(:c(:n:3([Pt]3(Cl)(n:2(:c(:c:1)(:c:1(:c(:c(:c(:c(:n3:1))))))))))))))))))))))).F([Sb](F)(F)(F)(F)([F-])).F([Sb](F)(F)(F)(F)([F-])) 1100753
---
> F([Sb](F)(F)(F)(F)([F-])).F([Sb](F)(F)(F)(F)([F-])).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C](N([C])([C](=O))).[C]1([C](c:2(:[c](:[c](:[c](:[c](:[c]:2(:[c]:2(:c1(:[c](:c:1([C]([C](c:3(:[c](:[c](:[c](:[c](:[c]:3(:[c]:1(:n:2))))(:[c]:1(:[c](:[c]:2(:[c]:3(:[c](:[c](:[c](:[c](:[n]:3([Pt]3(Cl)([n]:2(:[c](:[c]:1)(:[c]:1(:[c](:[c](:[c](:[c](:[n]3:1)))))))))))))))))))))))))(:[c]:1(:[c](:c(C([C])([C])([C]))(:[c](:c(C([C])([C])([C]))(:[c]:1)))))))))))(:[c]:1(:[c](:[c]:2(:[c]:3(:[c](:[c](:[c](:[c](:[n]:3([Pt]3(Cl)([n]:2(:[c](:[c]:1)(:[c]:1(:[c](:[c](:[c](:[c](:[n]3:1))))))))))))))))))))))) 1100753
tests/cases/smi_canonicalise_004.inp: FAILED:
1c1
< C(/C(=C(/C))).C(/C(=C(/C)))
---
> [C](/[C](=[C](/[C]))).[C](/[C](=[C](/[C])))
tests/cases/smi_canonicalise_005.inp: FAILED:
1c1
< Br([C@@]12(C(C(N([C@@]1(N(S([H]))(c([H])(:c2([H]))))([H]))([H]))([H])([H]))([H])([H]))).Br([C@]12(C(C(N([C@]1(N(S([H]))(c([H])(:c2([H]))))([H]))([H]))([H])([H]))([H])([H])))
---
> Br([C@@]12(C(C(N([C@@]1(N(S([H]))([c]([H])(:[c]2([H]))))([H]))([H]))([H])([H]))([H])([H]))).Br([C@]12(C(C(N([C@]1(N(S([H]))([c]([H])(:[c]2([H]))))([H]))([H]))([H])([H]))([H])([H])))
tests/cases/smi_canonicalise_006.inp: OK
tests/cases/smi_canonicalise_007.inp: FAILED:
1,4c1,4
< C1(=C(C(=C(C(=C1)))))
< c:1(:c(:c(:c(:c(:c(:c:1))))))
< c:1(:c(:c(:o(:c(:c:1)))))
< C(c:1(C)(:c(:c(:c(:c(:c:1))))))
---
> [C]1(=[C]([C](=[C]([C](=[C]1)))))
> [c]:1(:[c](:[c](:[c](:[c](:[c](:[c]:1))))))
> [c]:1(:[c](:[c](:[o](:[c](:[c]:1)))))
> [C]([c]:1([C])(:[c](:[c](:[c](:[c](:[c]:1))))))
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: FAILED:
1,2c1,2
< C([C@]1([C@@](C(O(P(=O)(O([H]))(O([H]))))([H])([H]))(C1(C([H])([H])(n:1(:c([H])(:n(:c:2(:c:1(:n(:c(Cl)(:n(:c:2(N(C([H])([H])([H]))([H]))))))))))))([H]))([H]))([H]))(O(P(=O)(O([H]))(O([H]))))([H])([H])
< C([C@]1([C@@](C(O(P(=O)(O([H]))(O([H]))))([H])([H]))(C1(C([H])([H])(n:1(:c([H])(:n(:c:2(:c:1(:n(:c(Cl)(:n(:c:2(N(C([H])([H])([H]))([H]))))))))))))([H]))([H]))([H]))(O(P(=O)(O([H]))(O([H]))))([H])([H])
---
> C([C@]1([C@@](C(O(P(=O)(O([H]))(O([H]))))([H])([H]))(C1(C([H])([H])([n]:1(:c([H])(:n(:[c]:2(:[c]:1(:n(:c(Cl)(:n(:c:2(N(C([H])([H])([H]))([H]))))))))))))([H]))([H]))([H]))(O(P(=O)(O([H]))(O([H]))))([H])([H])
> C([C@]1([C@@](C(O(P(=O)(O([H]))(O([H]))))([H])([H]))(C1(C([H])([H])([n]:1(:c([H])(:n(:[c]:2(:[c]:1(:n(:c(Cl)(:n(:c:2(N(C([H])([H])([H]))([H]))))))))))))([H]))([H]))([H]))(O(P(=O)(O([H]))(O([H]))))([H])([H])
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: FAILED:
3,4c3,4
< [H](c:1(:c([H])(:c([H])(:c([H])(:o(:c:1([H])))))))
< C([H])([H])([H])(c:1(C([H])([H])([H]))(:c([H])(:c([H])(:c([H])(:c([H])(:c:1([H])))))))
---
> [H](c:1(:c([H])(:c([H])(:c([H])(:[o](:c:1([H])))))))
> C([H])([H])([H])([c]:1(C([H])([H])([H]))(:c([H])(:c([H])(:c([H])(:c([H])(:c:1([H])))))))
tests/cases/smi_canonicalise_025.inp: FAILED:
1c1
< [H](c:1(:c([H])(:c([H])(:c:2(:c([H])(:c([H])(:c([H])(:c([H])(:c:2(:c:1([H])))))))))))
---
> [H](c:1(:c([H])(:c([H])(:[c]:2(:c([H])(:c([H])(:c([H])(:c([H])(:[c]:2(:c:1([H])))))))))))
tests/cases/smi_canonicalise_026.inp: FAILED:
1c1
< F(c:1(:c:2(:c([H])(:c([H])(:c([H])(:c:2(:c([H])(:c:1([H])))))))))
---
> F(c:1(:[c]:2(:c([H])(:c([H])(:c([H])(:[c]:2(:c([H])(:c:1([H])))))))))
tests/cases/smi_canonicalise_027.inp: FAILED:
1c1
< F(c:1(:c([H])(:c([H])(:n([H])(:c:1(F))))))
---
> F(c:1(:c([H])(:c([H])(:[n]([H])(:c:1(F))))))
tests/cases/smi_canonicalise_028.inp: FAILED:
1c1
< C(C(O([H]))([H])([H]))([H])([H])(c:1(:c:2(:c([H])(:c([H])(:c([H])(:c([H])(:c:2(:c([H])(:c([H])(:c:1([H]))))))))))).C(C(O([H]))([H])([H]))([H])([H])(c:1(:c:2(:c([H])(:c([H])(:c([H])(:c([H])(:c:2(:c([H])(:c([H])(:c:1([H])))))))))))
---
> C(C(O([H]))([H])([H]))([H])([H])(c:1(:[c]:2(:c([H])(:c([H])(:c([H])(:c([H])(:[c]:2(:c([H])(:c([H])(:c:1([H]))))))))))).C(C(O([H]))([H])([H]))([H])([H])(c:1(:[c]:2(:c([H])(:c([H])(:c([H])(:c([H])(:[c]:2(:c([H])(:c([H])(:c:1([H])))))))))))
tests/cases/smi_canonicalise_029.inp: OK
tests/cases/smi_isomorphism_001.sh: FAILED:
1c1
< [H](c:1(:c([H])(:c([H])(:c:2(:c(:c:1([H]))(:c:1(:c([H])(:c([H])(:c([H])(:c([H])(:c:2:1)))))))))))
---
> [H](c:1(:c([H])(:c([H])(:[c]:2(:[c](:c:1([H]))(:[c]:1(:c([H])(:c([H])(:c([H])(:c([H])(:[c]:2:1)))))))))))
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: FAILED:
1c1
< scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties of 'C(C(C(O)(=O))(N))', 2 vs. 1
---
> scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties of '[C]([C](C([O])(=O))([N]))', 2 vs. 1
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: FAILED:
25c25
< scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties of 'C1(C(C(N(C2(C(C(C(C(C2([H])([H]))([H])([H]))([H])([H]))([H])([H]))(N(C(C2(C(C(C(C(C2([H]))([H]))([H]))([H]))(Cl)))([H])))([H]))([H])))([H]))(C(C(C(C1([H]))([H]))([H]))([H])))(Cl)', 1 vs. 2
---
> scripts/smi_isomorphism: -(1) XXXXXXX: different number of moieties of '[C]1([C]([C]([N](C2(C(C(C(C(C2([H])([H]))([H])([H]))([H])([H]))([H])([H]))([N]([C]([C]2([C]([C]([C]([C]([C]2([H]))([H]))([H]))([H]))(Cl)))([H])))([H]))([H])))([H]))([C]([C]([C]([C]1([H]))([H]))([H]))([H])))(Cl)', 1 vs. 2
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:
2c2
< scripts/smi_isomorphism: -(1) 2000891: different number of moieties of 'C1(C(C(C(C2(C1(C(C(C(C2([H]))(S(O)(O)(O(C1(C(C(C(C(C1(F)([H]))([H])([H]))([H])([H]))([H])([H]))([H])([H]))([H])))))([H]))([H]))))([H]))([H]))([H]))([H])', 2 vs. 1
---
> scripts/smi_isomorphism: -(1) 2000891: different number of moieties of '[C]1([C]([C]([C]([C]2([C]1([C]([C]([C]([C]2([H]))(S([O])([O])(O(C1(C(C(C(C(C1(F)([H]))([H])([H]))([H])([H]))([H])([H]))([H])([H]))([H])))))([H]))([H]))))([H]))([H]))([H]))([H])', 2 vs. 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
find tests/outputs -name '*.diff' -a -size +0 | xargs --no-run-if-empty -i echo FAILED: {}
FAILED: tests/outputs/smi_canonicalise_028.diff
FAILED: tests/outputs/smi_isomorphism_032.diff
FAILED: tests/outputs/smi_canonicalise_027.diff
FAILED: tests/outputs/smi_canonicalise_024.diff
FAILED: tests/outputs/smi_canonicalise_023.diff
FAILED: tests/outputs/smi_isomorphism_013.diff
FAILED: tests/outputs/cml-to-smi_004.diff
FAILED: tests/outputs/smi_canonicalise_025.diff
FAILED: tests/outputs/smi_canonicalise_026.diff
FAILED: tests/outputs/smi_canonicalise_002.diff
FAILED: tests/outputs/sdf-to-smi_015.diff
FAILED: tests/outputs/smi_canonicalise_004.diff
FAILED: tests/outputs/sdf-to-smi_006.diff
FAILED: tests/outputs/smi_canonicalise_017.diff
FAILED: tests/outputs/cml-to-smi_008.diff
FAILED: tests/outputs/sdf-to-smi_005.diff
FAILED: tests/outputs/smi_canonicalise_001.diff
FAILED: tests/outputs/smi_canonicalise_003.diff
FAILED: tests/outputs/smi_isomorphism_022.diff
FAILED: tests/outputs/sdf-to-smi_001.diff
FAILED: tests/outputs/smi_canonicalise_006.diff
FAILED: tests/outputs/sdf-to-smi_011.diff
find tests/outputs -name '*.diff' -a -size +0 | xargs --no-run-if-empty false # Detect test failures
make[1]: *** [debian/rules:38: override_dh_auto_test] Error 123
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202412/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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