Your message dated Sun, 11 Dec 2022 22:04:45 +0000
with message-id <e1p4urb-00bmt8...@fasolo.debian.org>
and subject line Bug#1025887: fixed in biojava4-live 4.2.12+dfsg-8
has caused the Debian Bug report #1025887,
regarding FTBFS: ambiguous method call
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
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immediately.)
--
1025887: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1025887
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: biojava4-live
Version: 4.2.12+dfsg-7
Severity: serious
Tags: ftbfs patch
Dear Maintainer,
biojava4-live currently fails to build with the following error message:
compile:
[mkdir] Created dir:
/build/1st/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes
[javac]
/build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml:86:
warning: 'includeantruntime' was not set, defaulting to
build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 483 source files to
/build/1st/biojava4-live-4.2.12+dfsg/build/biojava4-structure/classes
[javac]
/build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:239:
error: reference to newFileSystem is ambiguous
[javac] try (FileSystem fs =
FileSystems.newFileSystem(m_zipFile, null)) {
[javac] ^
[javac] both method newFileSystem(Path,ClassLoader) in FileSystems
and method newFileSystem(Path,Map<String,?>) in FileSystems match
[javac]
/build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:296:
error: reference to newFileSystem is ambiguous
[javac] try (FileSystem zipfs =
FileSystems.newFileSystem(zipFile, null)) {
[javac] ^
[javac] both method newFileSystem(Path,ClassLoader) in FileSystems
and method newFileSystem(Path,Map<String,?>) in FileSystems match
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use or override a deprecated API that
is marked for removal.
[javac] Note: Recompile with -Xlint:removal for details.
[javac] Note:
/build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java
uses unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 2 errors
(see
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/biojava4-live.html
for details)
When casting the null value to match one of the signatures this resolves
the build error. See the attached patch. I wasn't able to find the exact
upstream commit to reference since the file has been moved around, but
the patch is based on latest upstream and how they have chosen to
resolve the issue.
-- System Information:
Debian Release: bookworm/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 6.0.0-5-amd64 (SMP w/3 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--
mvh / best regards
Hans Joachim Desserud
http://desserud.org
Description: Add explicit cast to fix ambiguos method call error
Taken from upstream to match expected method call
https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
---
Origin: upstream
Forwarded: not-needed
Last-Update: 2022-12-11
--- biojava4-live-4.2.12+dfsg.orig/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
+++ biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -236,7 +236,7 @@ public class ZipChemCompProvider impleme
final String filename = "chemcomp/" + recordName+".cif.gz";
// try with resources block to read from the filesystem.
- try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, null)) {
+ try (FileSystem fs = FileSystems.newFileSystem(m_zipFile, (ClassLoader)null)) {
Path cif = fs.getPath(filename);
if (Files.exists(cif)) {
@@ -293,7 +293,7 @@ public class ZipChemCompProvider impleme
*/
// Copy in each file.
- try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, null)) {
+ try (FileSystem zipfs = FileSystems.newFileSystem(zipFile, (ClassLoader)null)) {
Files.createDirectories(pathWithinArchive);
for (File f : files) {
if (!f.isDirectory() && f.exists()) {
--- End Message ---
--- Begin Message ---
Source: biojava4-live
Source-Version: 4.2.12+dfsg-8
Done: Pierre Gruet <p...@debian.org>
We believe that the bug you reported is fixed in the latest version of
biojava4-live, 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 1025...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <p...@debian.org> (supplier of updated biojava4-live 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 11 Dec 2022 22:19:23 +0100
Source: biojava4-live
Architecture: source
Version: 4.2.12+dfsg-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <p...@debian.org>
Closes: 1025887
Changes:
biojava4-live (4.2.12+dfsg-8) unstable; urgency=medium
.
* Fixing ambiguous method call to newFileSystem, thanks to Hans Joachim
Desserud! (Closes: #1025887)
* Correcting the Lintian override for embedded JS after a change in Lintian
syntax
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