vdjtools: FTBFS with default Java 21

Bug #2054054 reported by Vladimir Petko
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
vdjtools (Debian)
Fix Released
Unknown
vdjtools (Ubuntu)
New
Undecided
Unassigned

Bug Description

The package vdjtools ftbfs with default Java 21.
The relevant part of the build log:
---------------
Compiling with JDK Java compiler API.
warning: [options] bootstrap class path not set in conjunction with -source 8
warning: [options] source value 8 is obsolete and will be removed in a future release
warning: [options] target value 8 is obsolete and will be removed in a future release
warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
/<<PKGBUILDDIR>>/build/tmp/compileGroovy/groovy-java-stubs/com/antigenomics/vdjtools/misc/ExecUtil.java:16: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal
public static final int THREADS = new java.lang.Integer((int)0);
                                  ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/LinkedListExt.java:102: error: types Deque<E> and List<E> are incompatible;
public class LinkedListExt<E>
       ^
  both define reversed(), but with unrelated return types
  where E is a type-variable:
    E extends Object declared in class LinkedListExt
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:285: warning: Unsafe is internal proprietary API and may be removed in a future release
    private static final sun.misc.Unsafe unsafe = getUnsafe();
                                 ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:311: warning: Unsafe is internal proprietary API and may be removed in a future release
    private static sun.misc.Unsafe getUnsafe() {
                           ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:313: warning: Unsafe is internal proprietary API and may be removed in a future release
            return sun.misc.Unsafe.getUnsafe();
                           ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:317: warning: Unsafe is internal proprietary API and may be removed in a future release
                    (new java.security.PrivilegedExceptionAction<sun.misc.Unsafe>() {
                                                                         ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:318: warning: Unsafe is internal proprietary API and may be removed in a future release
                        public sun.misc.Unsafe run() throws Exception {
                                       ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:319: warning: Unsafe is internal proprietary API and may be removed in a future release
                            Class<sun.misc.Unsafe> k = sun.misc.Unsafe.class;
                                          ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:319: warning: Unsafe is internal proprietary API and may be removed in a future release
                            Class<sun.misc.Unsafe> k = sun.misc.Unsafe.class;
                                                               ^
/<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java:316: warning: [removal] AccessController in java.security has been deprecated and marked for removal
            return java.security.AccessController.doPrivileged
                                ^
Note: /<<PKGBUILDDIR>>/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 error
13 warnings
startup failed:
Compilation failed; see the compiler error output for details.

1 error

:compileGroovy FAILED
:compileGroovy (Thread[#41,Task worker for ':',5,main]) completed. Took 3.381 secs.

Changed in vdjtools (Debian):
status: Unknown → New
Changed in vdjtools (Debian):
status: New → Fix Released
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