Your message dated Fri, 16 Feb 2024 17:05:50 +0000
with message-id <[email protected]>
and subject line Bug#1057537: fixed in vdjtools 1.2.1+git20190311+repack-2
has caused the Debian Bug report #1057537,
regarding vdjtools: FTBFS with default Java 21
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1057537: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1057537
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: vdjtools
Version: 1.2.1+git20190311+repack-1
Severity: important
Tags: ftbfs
User: [email protected]
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warning: [options] source value 8 is obsolete and will be removed in a future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warning: [options] target value 8 is obsolete and will be removed in a future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
--- End Message ---
--- Begin Message ---
Source: vdjtools
Source-Version: 1.2.1+git20190311+repack-2
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
vdjtools, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated vdjtools 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 16 Feb 2024 10:14:48 +0100
Source: vdjtools
Binary: libvdjtools-java vdjtools
Architecture: source all
Version: 1.2.1+git20190311+repack-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
libvdjtools-java - Java library of vdjtools
vdjtools - framework for post-analysis of B/T cell repertoires
Closes: 1057537
Changes:
vdjtools (1.2.1+git20190311+repack-2) unstable; urgency=medium
.
* Team upload.
.
[ Vladimir Petko ]
* d/p/jdk-remove-collection.patch: remove unused collection class to
resolve Java 21 ftbfs (Closes: #1057537).
.
[ Andreas Tille ]
* Standards-Version: 4.6.2 (routine-update)
Checksums-Sha1:
23d5922615d6f6955c28cb9d90edeb8f9f804946 2422
vdjtools_1.2.1+git20190311+repack-2.dsc
ef86c267c04e394b8915be2c4e9c682548b6c5cc 13300
vdjtools_1.2.1+git20190311+repack-2.debian.tar.xz
130bf3ed57801dc2273f275191dae6cbbee439ae 1069152
libvdjtools-java_1.2.1+git20190311+repack-2_all.deb
32c0262c3c73c9751346bdc66bb446936792e4da 43252
vdjtools_1.2.1+git20190311+repack-2_all.deb
5535898b3942db7ac44b86727cee593b9f427fba 17178
vdjtools_1.2.1+git20190311+repack-2_amd64.buildinfo
Checksums-Sha256:
144106812857ce29ad608144ac9f0bad9114bee1c65a30dca1158e7d9f298a2e 2422
vdjtools_1.2.1+git20190311+repack-2.dsc
3f9f04a59726b12fe61f796baf998e6ec153733c8a1de92bff6da09c59a8923a 13300
vdjtools_1.2.1+git20190311+repack-2.debian.tar.xz
06831699ac26c9fc80abf09a6d963275dd18e69d52d8a59f0d1d74371e9f9739 1069152
libvdjtools-java_1.2.1+git20190311+repack-2_all.deb
fd05df7308815b61cceb46d9c2866d82717a4b6d589538e8f0c37811f6c1ebfd 43252
vdjtools_1.2.1+git20190311+repack-2_all.deb
11ad2a8a386559e44dbcd34a340d03b00be11629ef49d450024cb649e2aa0832 17178
vdjtools_1.2.1+git20190311+repack-2_amd64.buildinfo
Files:
1fbfa83cbf9940d78ebee8de4a6d6f34 2422 non-free/science optional
vdjtools_1.2.1+git20190311+repack-2.dsc
32e22d22e8d691a50b7d1fc9cf09d174 13300 non-free/science optional
vdjtools_1.2.1+git20190311+repack-2.debian.tar.xz
346c40569f03e68ffff403d97e7a29db 1069152 non-free/java optional
libvdjtools-java_1.2.1+git20190311+repack-2_all.deb
8e0604f51301c54ccfc34cd7ec5a3d20 43252 non-free/science optional
vdjtools_1.2.1+git20190311+repack-2_all.deb
5a4f529058296d0c8504c1751c7af623 17178 non-free/science optional
vdjtools_1.2.1+git20190311+repack-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=1KCk
-----END PGP SIGNATURE-----
pgpUliNcKKsVy.pgp
Description: PGP signature
--- End Message ---
