[Debian-med-packaging] Bug#913566: htsjdk FTBFS with OpenJDK 11

[Adrian Bunk]

Source: htsjdk
Version: 2.16.1+dfsg-1
Severity: serious
Tags: ftbfs

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

...
Compiling with JDK Java compiler API.
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:34: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlElement;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:35: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlRootElement;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:36: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlTransient;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:26: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlAttribute;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:27: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlRootElement;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:28: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlValue;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:26: error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlTransient;
                                ^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:36: error: cannot find symbol
@XmlTransient /* don't consider this class for XML-serialization */
 ^
  symbol: class XmlTransient
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:41: error: cannot find symbol
@XmlRootElement(name="Reference")
 ^
  symbol: class XmlRootElement
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:44: error: cannot find symbol
@XmlRootElement(name="References")
 ^
  symbol: class XmlRootElement
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:51: error: cannot find symbol
    @XmlElement(name="Reference")
     ^
  symbol:   class XmlElement
  location: class SAMSequenceDictionary
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:63: error: cannot find symbol
    @XmlTransient //we use the field instead of getter/setter
     ^
  symbol:   class XmlTransient
  location: class SAMSequenceDictionary
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:103: error: cannot find symbol
    @XmlValue
     ^
  symbol:   class XmlValue
  location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:117: error: cannot find symbol
    @XmlAttribute(name="length")
     ^
  symbol:   class XmlAttribute
  location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:121: error: cannot find symbol
    @XmlAttribute(name="assembly")
     ^
  symbol:   class XmlAttribute
  location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:125: error: cannot find symbol
    @XmlAttribute(name="species")
     ^
  symbol:   class XmlAttribute
  location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:129: error: cannot find symbol
    @XmlAttribute(name="md5")
     ^
  symbol:   class XmlAttribute
  location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:136: error: cannot find symbol
    @XmlAttribute(name="index")
     ^
  symbol:   class XmlAttribute
  location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/cram/structure/EncodingParams.java:36: error: package javax.xml.bind does not exist
        return id.name() + ":" + javax.xml.bind.DatatypeConverter.printHexBinary(Arrays.copyOfRange(params, 0, Math.max(20, params.length)));
                                               ^
Note: Some input files use or override 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.
19 errors