Bug#1025887: FTBFS: ambiguous method call

[Pierre Gruet]

Control: tags -1 pending

Dear Hans,


> 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]

> 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]

> 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:

> uses unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [javac] 2 errors
>
> (see

On Sun, 11 Dec 2022 11:23:19 +0100 Hans Joachim Desserud <deb...@desserud.org> wrote: > /build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:239: > /build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java:296: > /build/1st/biojava4-live-4.2.12+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java > 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.



Best regards,

--
Pierre

Thanks a lot for your report and patch, fixing bugs this way is so easy :) An upload with your fix is coming soon.

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