#1139502 cmlxom: FTBFS: CMLBuilderTest.testBuildFile:156 OldNodeFactory validation expected:<...DOCTYPE root "null".[ at line 27, column 50]> but was:<...DOCTYPE root "null".[]>

Package:
src:cmlxom
Source:
src:cmlxom
Submitter:
Santiago Vila
Date:
2026-06-12 11:07:03 UTC
Severity:
normal
Tags:
#1139502#5
Date:
2026-06-09 10:29:23 UTC
From:
To:
Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202606/

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 cannot 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 add an affects on src:cmlxom, so that this is still
visible in the BTS web page for this package.

Thanks.
--------------------------------------------------------------------------------
[...]
[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLJoinTest
[INFO] Running org.xmlcml.cml.element.main.CMLBuilderTest
[ERROR] Tests run: 3, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.007 s <<< FAILURE! - in org.xmlcml.cml.element.main.CMLBuilderTest
[ERROR] testBuildFile(org.xmlcml.cml.element.main.CMLBuilderTest)  Time elapsed: 0.007 s  <<< FAILURE!
junit.framework.ComparisonFailure: OldNodeFactory validation expected:<...DOCTYPE root "null".[ at line 27, column 50]> but was:<...DOCTYPE root "null".[]>
	at org.xmlcml.cml.element.main.CMLBuilderTest.testBuildFile(CMLBuilderTest.java:156)

[INFO] Running org.xmlcml.cml.element.main.CMLAtomTypeTest
[INFO] Tests run: 45, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLAtomTypeTest
[INFO] Running org.xmlcml.cml.element.main.CMLBandListTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLBandListTest
[INFO] Running org.xmlcml.cml.element.main.CMLMetadataTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLMetadataTest
[INFO] Running org.xmlcml.cml.element.main.CMLDefinitionTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLDefinitionTest
[INFO] Running org.xmlcml.cml.element.main.CMLBasisSetTest
[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLBasisSetTest
[INFO] Running org.xmlcml.cml.element.main.CMLAngleTest
[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.xmlcml.cml.element.main.CMLAngleTest
[INFO] Running org.xmlcml.cml.element.main.CMLTorsionTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.main.CMLTorsionTest
[INFO] Running org.xmlcml.cml.element.main.CMLSymmetryTest
[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 s - in org.xmlcml.cml.element.main.CMLSymmetryTest
[INFO] Running org.xmlcml.cml.element.main.CMLAbundanceTest
[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.xmlcml.cml.element.main.CMLAbundanceTest
[INFO] Running org.xmlcml.cml.element.main.ElementsTest
Index 2 out of bounds for length 2
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.xmlcml.cml.element.main.ElementsTest
[INFO] Running org.xmlcml.cml.element.main.CMLArrayListTest
[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.xmlcml.cml.element.main.CMLArrayListTest
[INFO] Running org.xmlcml.cml.element.main.CMLTableTest
[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 s - in org.xmlcml.cml.element.main.CMLTableTest
[INFO] Running org.xmlcml.cml.element.main.CMLCrystalTest
[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.xmlcml.cml.element.main.CMLCrystalTest
[INFO] Running org.xmlcml.cml.element.lite.CMLArrayTest
[INFO] Tests run: 51, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s - in org.xmlcml.cml.element.lite.CMLArrayTest
[INFO] Running org.xmlcml.cml.element.lite.CMLPeakListTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.lite.CMLPeakListTest
[INFO] Running org.xmlcml.cml.element.lite.CMLAtomTest
[INFO] Tests run: 39, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.xmlcml.cml.element.lite.CMLAtomTest
[INFO] Running org.xmlcml.cml.element.lite.CMLMoleculeTest
[INFO] Tests run: 64, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 s - in org.xmlcml.cml.element.lite.CMLMoleculeTest
[INFO] Running org.xmlcml.cml.element.lite.CMLBondArrayTest
[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.xmlcml.cml.element.lite.CMLBondArrayTest
[INFO] Running org.xmlcml.cml.element.lite.CMLPeakStructureTest
[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.lite.CMLPeakStructureTest
[INFO] Running org.xmlcml.cml.element.lite.CMLPeakTest
[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.lite.CMLPeakTest
[INFO] Running org.xmlcml.cml.element.lite.CMLBondStereoTest
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.lite.CMLBondStereoTest
[INFO] Running org.xmlcml.cml.element.lite.CMLPropertyTest
[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in org.xmlcml.cml.element.lite.CMLPropertyTest
[INFO] Running org.xmlcml.cml.element.lite.CMLBondTest
[INFO] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.xmlcml.cml.element.lite.CMLBondTest
[INFO] Running org.xmlcml.cml.element.lite.CMLFormulaTest
[INFO] Tests run: 53, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.xmlcml.cml.element.lite.CMLFormulaTest
[INFO] Running org.xmlcml.cml.element.lite.CMLScalarTest
[WARNING] Tests run: 31, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.023 s - in org.xmlcml.cml.element.lite.CMLScalarTest
[INFO] Running org.xmlcml.cml.element.lite.CMLAtomParityTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.xmlcml.cml.element.lite.CMLAtomParityTest
[INFO] Running org.xmlcml.cml.element.lite.CMLAtomArrayTest
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 s - in org.xmlcml.cml.element.lite.CMLAtomArrayTest
[INFO] Running org.xmlcml.molutil.test.ChemicalElementTest
[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.xmlcml.molutil.test.ChemicalElementTest
[INFO]
[INFO] Results:
[INFO]
[ERROR] Failures:
[ERROR]   CMLBuilderTest.testBuildFile:156 OldNodeFactory validation expected:<...DOCTYPE root "null".[ at line 27, column 50]> but was:<...DOCTYPE root "null".[]>
[INFO]
[ERROR] Tests run: 1235, Failures: 1, Errors: 0, Skipped: 2
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  33.393 s
[INFO] Finished at: 2026-06-08T22:06:53Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.3:test (default-test) on project cmlxom: There are test failures.
[ERROR]
[ERROR] Please refer to /<<PKGBUILDDIR>>/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
dh_auto_test: error: /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/<<PKGBUILDDIR>> -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<PKGBUILDDIR>>/debian -Dmaven.repo.local=/<<PKGBUILDDIR>>/debian/maven-repo --batch-mode test returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------

#1139502#10
Date:
2026-06-12 11:04:28 UTC
From:
To:
We believe that the bug you reported is fixed in the latest version of
cmlxom, 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 1139502@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <merkys@debian.org> (supplier of updated cmlxom 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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Fri, 12 Jun 2026 06:43:50 -0400
Source: cmlxom
Architecture: source
Version: 4.18-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Java Maintainers <pkg-java-maintainers@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Closes: 1139502
Changes:
 cmlxom (4.18-2) unstable; urgency=medium
 .
   * Depend on libxom-java >= 1.4.4 (Closes: #1139502)
Checksums-Sha1:
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 0423384d6802872226d933c0e4d8525247708c66 3092 cmlxom_4.18-2.debian.tar.xz
 00b24590d357cb9173bc0a0aa604028c80054a5d 14815 cmlxom_4.18-2_source.buildinfo
Checksums-Sha256:
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 7710d146383057837e25d6024ac1fdda33f7062010d687672710588c1b08ece4 3092 cmlxom_4.18-2.debian.tar.xz
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Files:
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 aa5257a9e4c80847ac2007da8fb8359f 3092 java optional cmlxom_4.18-2.debian.tar.xz
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