[Debian-med-packaging] Bug#1057537: vdjtools: FTBFS with default Java 21

[Vladimir Petko]

Source: vdjtools
Version: 1.2.1+git20190311+repack-1
Severity: important
Tags: ftbfs
User: debian-java at lists.debian.org
Usertags: default-java21

Dear Maintainers,

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warning: [options] source value 8 is obsolete and will be removed in a future release
warning: [options] target value 8 is obsolete and will be removed in a future release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.

---------------


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

Kernel: Linux 6.5.0-13-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