[Debian-med-packaging] Bug#1025887: FTBFS: ambiguous method call

[Hans Joachim Desserud]

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
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