Bug#1108586: openchemlib: FTBFS with default Java 25

Tue Jul 1 05:23:52 BST 2025

Source: openchemlib
Version: 2023.1.1+dfsg-1
Severity: normal
Tags: ftbfs
Usertags: default-java25

Dear Maintainers,

The package openchemlib ftbfs with default Java 25.
The relevant part of the build log:
---------------
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ openchemlib ---
[INFO] Recompiling the module because of changed source code.
[INFO] Compiling 928 source files with javac [debug target 1.8] to target/classes
[INFO] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/jfx/gui/misc/ClipboardHelper.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/jfx/gui/misc/ClipboardHelper.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/fx/FXComboBox.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/fx/FXComboBox.java: Recompile with -Xlint:unchecked for details.
[INFO] -------------------------------------------------------------
[WARNING] COMPILATION WARNING :
[INFO] -------------------------------------------------------------
[WARNING] bootstrap class path is not set in conjunction with -source 8
  not setting the bootstrap class path may lead to class files that cannot run on JDK 8
    --release 8 is recommended instead of -source 8 -target 1.8 because it sets the bootstrap class path automatically
[WARNING] source value 8 is obsolete and will be removed in a future release
[WARNING] target value 8 is obsolete and will be removed in a future release
[WARNING] To suppress warnings about obsolete options, use -Xlint:-options.
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/HeaderPaintHelper.java:[41,21] java.security.AccessControlException in java.security has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/util/datamodel/IntVec.java:[1083,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java:[257,43] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java:[293,91] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java:[308,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java:[328,75] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java:[329,77] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/editor/GenericEditorArea.java:[2153,84] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/editor/GenericEditorArea.java:[2187,102] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/TextDrawingObject.java:[148,71] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MarkushStructure.java:[135,40] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MarkushStructure.java:[171,44] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/calc/Matrix.java:[644,28] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/calc/Matrix.java:[1393,20] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/calc/Matrix.java:[2810,20] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MolfileParser.java:[1110,35] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MolfileParser.java:[1110,65] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MolfileParser.java:[1117,35] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MolfileParser.java:[1117,65] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MolfileParser.java:[1121,81] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/MolfileParser.java:[1126,81] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/Molecule3D.java:[386,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/Molecule3D.java:[388,45] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/io/DWARFileParser.java:[294,45] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/io/DWARFileParser.java:[352,70] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java:[300,74] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java:[302,62] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java:[302,82] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java:[304,62] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java:[304,82] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/util/SizeOf.java:[58,24] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/util/SizeOf.java:[76,20] runFinalization() in java.lang.Runtime has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/io/StringReadChannel.java:[153,21] finalize() in java.lang.Object has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/JDrawArea.java:[2233,84] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/JDrawArea.java:[2268,102] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/properties/complexity/ExhaustiveFragmentsStatistics.java:[284,21] finalize() in java.lang.Object has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/properties/complexity/ExhaustiveFragmentsStatistics.java:[293,22] finalize() in java.lang.Object has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[628,48] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[755,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[757,30] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[763,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[771,56] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[772,55] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java:[773,54] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/StructureSearch.java:[340,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/util/BinaryEncoder.java:[158,21] finalize() in java.lang.Object has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/forcefield/mmff/SortedPair.java:[62,16] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/forcefield/mmff/SortedPair.java:[62,44] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/AtomTypeList.java:[107,36] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/AtomTypeList.java:[108,31] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/AtomTypeList.java:[262,35] Long(long) in java.lang.Long has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/PeriodicTable.java:[195,46] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/calc/BinarySOM.java:[78,49] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/calc/MatrixFunctions.java:[644,25] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/calc/MatrixFunctions.java:[645,25] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/smile/stat/distribution/GaussianDistribution.java:[162,25] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/reaction/ReactionSearch.java:[466,66] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/io/ODEFileParser.java:[196,53] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/forcefield/mmff/Vector3.java:[182,16] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/forcefield/mmff/Vector3.java:[183,15] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/forcefield/mmff/Vector3.java:[184,15] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/optimization/Lnsrch.java:[152,45] Double(double) in java.lang.Double has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/gui/HeaderPaintHelper.java:[52,24] java.security.AccessControlException in java.security has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/UniqueStringList.java:[66,39] Integer(int) in java.lang.Integer has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/properties/complexity/MolecularComplexityCalculator.java:[72,21] finalize() in java.lang.Object has been deprecated and marked for removal
[WARNING] /<<PKGBUILDDIR>>/src/main/java/com/actelion/research/chem/properties/complexity/MolecularComplexityCalculator.java:[74,22] finalize() in java.lang.Object has been deprecated and marked for removal
[INFO] 70 warnings
[INFO] -------------------------------------------------------------
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /<<PKGBUILDDIR>>/src/main/java/smile/math/Math.java:[2147,48] unreported exception java.lang.InterruptedException; must be caught or declared to be thrown
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  9.016 s
[INFO] Finished at: 2025-06-11T20:29:02Z
---------------

-- System Information:
Debian Release: trixie/sid
  APT prefers plucky-updates
  APT policy: (500, 'plucky-updates'), (500, 'plucky-security'), (500, 'plucky')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.14.0-22-generic (SMP w/32 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled