[Debian-med-packaging] Bug#894289: Please have a look [bunk at debian.org: Bug#894289: htsjdk FTBFS with openjdk-9]

[Andreas Tille]

Hi,

I've upgraded Git to the latest upstream version but the bug persists.
Could you please have a look and upload to experimental since we need
to update picard-tools (also buggy) as well and should do this probably
in a mini tranition?

Thanks

       Andreas.

----- Forwarded message from Adrian Bunk <bunk at debian.org> -----

Date: Wed, 28 Mar 2018 14:25:53 +0300
From: Adrian Bunk <bunk at debian.org>
To: Debian Bug Tracking System <submit at bugs.debian.org>
Subject: Bug#894289: htsjdk FTBFS with openjdk-9
X-Debian-PR-Message: report 894289
X-Debian-PR-Package: src:htsjdk
X-Debian-PR-Keywords: 
X-Debian-PR-Source: htsjdk

Source: htsjdk
Version: 2.8.1+dfsg-2
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/htsjdk.html

...
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:35: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlElement;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:36: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlRootElement;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:37: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlTransient;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:35: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlAttribute;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:36: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlRootElement;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:37: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlValue;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
/build/1st/htsjdk-2.8.1+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:31: error: package javax.xml.bind.annotation is not visible
import javax.xml.bind.annotation.XmlTransient;
                     ^
  (package javax.xml.bind.annotation is declared in module java.xml.bind, which is not in the module graph)
7 errors

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