Re: [Help] Build issue of latest version of libsbml (probably Java compatibility issue)

[Pierre Gruet]

Hi Andreas,

Le 25/11/2022 à 10:57, Andreas Tille a écrit :

Hi,

I just realised that libsbml moved to Github.  After fixing the watch
file I tried to package the latest upstream version.  Unfortunately
the build fails and I see the lines

/builds/med-team/libsbml/debian/output/source_dir/src/bindings/java/AutoTestRunner.java:48:
 error: package org.sbml.libsbml.test does not exist
import org.sbml.libsbml.test.*;
^
Note: 
/builds/med-team/libsbml/debian/output/source_dir/src/bindings/java/AutoTestRunner.java
 uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
1 error

in the build log[1].

Any help would be appreciated.

Would you like to take over?

Done! Indeed there was an import of an empty set of Java classes, I repaired this. Also I added a missing #include in another set of bindings. I submitted my patches upstream. Now dh_auto_build succeeds but there is a whole bunch of reports for dh_missing, see relevant excerpt at the end of this email (Salsa CI job stopped outputting before this step).

Kind regards
    Andreas.

Best regards,

--
Pierre

------------------------------8<-------------------------------------

   debian/rules override_dh_missing
make[1]: Entering directory '/<<PKGBUILDDIR>>'
find debian -name test.xml -delete
rm -f debian/tmp/usr/share/libsbml/*.txt \
      debian/tmp/usr/share/libsbml/README*
dh_missing

dh_missing: error: missing files, aborting

          (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz)

        paths to debian/not-installed.


        to ensure it works on all architectures (see #961104).
make[1]: *** [debian/rules:116: override_dh_missing] Error 25

dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/compareFiles.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/runTests.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/algebraicRules.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/both.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/convertedFormulas.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/convertedFormulas2.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/convertedFormulasL2.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/createdAnnotation.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/createdAnnotationL2.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/csymbolAvogadro.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/csymbolDelay.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/csymbolTime-reaction-l2.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/csymbolTime.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/errors.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fatal.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbc.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbcL3V2V1.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbcL3V2V2.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbcV2.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbcV2Labels.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbc_groups.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbc_qual.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/fbc_qual_groups.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/funcDefsWithInitialAssignments.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/functionDefinition.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/groups-example1.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/groups_qual.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/initialAssignments.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l1v1-branch.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l1v1-minimal.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l1v1-rules.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l1v1-units.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l1v1.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l1v2-all.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v1-all.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v1-allelements.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v1-assignment.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v2-all.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v2-newComponents.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v2-newelements.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v3-all.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v3-newMath.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v3-newelements.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v4-all.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l2v5-all.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l3v1core.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l3v2-empty-event.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l3v2-empty-math.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l3v2-newmath.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l3v2-no-model.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/l3v2core.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/math_no_arguments.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/missing_out.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/nestedPiecewise.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/nonLogicals.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/none.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/notes_annotations.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/outGP00.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/outGP01.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/outGP10.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/outGP11.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/piecewise.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/qual.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/rateRules.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/readerror.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/sparseStoichiometry.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/species.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/test-greek.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/test-data/warn.xml exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testBinding.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testCVTerms.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testGetSBMLDefaultStruct.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testIsSBMLModel.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testMissingOutput.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testOutput.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFlags.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile1.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile10.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile11.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile12.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile13.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile14.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile15.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile16.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile2.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile3.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile4.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile5.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile6.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile7.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile8.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFile9.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFileFbc1.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadFromFileFbc2.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadWriteGeneProductIds.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testReadWriteGeneProducts.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/x86_64-linux-gnu/octave/site/oct/x86_64-pc-linux-gnu/test/testVersionInformation.m exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/cmake/Modules/FindBZ2.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/cmake/Modules/FindLIBSBML.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/cmake/Modules/FindLIBXML.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/cmake/Modules/FindZLIB.cmake exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: libsbml5 (2), libsbml5-cil (2), libsbml5-cil-doc (0), libsbml5-dev (5), libsbml5-doc (0), libsbml5-examples (0), libsbml5-java (2), libsbml5-octave (20), libsbml5-perl (1), libsbml5-perl-doc (0), python3-sbml5 (1), python3-sbml5-doc (0) * dh_installdocs: libsbml5 (4), libsbml5-cil (0), libsbml5-cil-doc (1), libsbml5-dev (0), libsbml5-doc (4), libsbml5-examples (0), libsbml5-java (0), libsbml5-octave (0), libsbml5-perl (0), libsbml5-perl-doc (1), python3-sbml5 (0), python3-sbml5-doc (1) * dh_installexamples: libsbml5 (0), libsbml5-cil (0), libsbml5-cil-doc (0), libsbml5-dev (0), libsbml5-doc (0), libsbml5-examples (27), libsbml5-java (0), libsbml5-octave (0), libsbml5-perl (0), libsbml5-perl-doc (0), python3-sbml5 (0), python3-sbml5-doc (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the Remember to be careful with paths containing "x86_64-linux-gnu", where you might need to use a wildcard or (assuming compat 13+) e.g. ${DEB_HOST_MULTIARCH} in debian/not-installed

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