[Debian-med-packaging] Build time failures for new version of biojava4-live 4.2.12

[Andreas Tille]

Hi,

when trying to build biojava4-live[1] I get:

...
Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml

compile:
    [mkdir] Created dir: /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:93: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 32 source files to /build/biojava4-live-4.2.12+dfsg/build/biojava4-aa-prop/classes
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:23: error: package javax.xml.bind.annotation does not exist
    [javac] import javax.xml.bind.annotation.XmlAccessType;
    [javac]                                 ^
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:24: error: package javax.xml.bind.annotation does not exist
    [javac] import javax.xml.bind.annotation.XmlAccessorType;
    [javac]                                 ^
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:25: error: package javax.xml.bind.annotation does not exist
    [javac] import javax.xml.bind.annotation.XmlElement;
    [javac]                                 ^
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:26: error: package javax.xml.bind.annotation does not exist
    [javac] import javax.xml.bind.annotation.XmlRootElement;
    [javac]                                 ^
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java:33: error: cannot find symbol
    [javac] @XmlRootElement(name="compoundtable", namespace="http://biojava.org")
    [javac]  ^
    [javac]   symbol: class XmlRootElement
...
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java:148: error: cannot find symbol
    [javac]             Unmarshaller u2 = jc2.createUnmarshaller();
    [javac]             ^
    [javac]   symbol:   class Unmarshaller
    [javac]   location: class PeptidePropertiesImpl
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:34: error: method does not override or implement a method from a         supertype
    [javac]     @Override
    [javac]     ^
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: error: cannot find symbol
    [javac]             if (ve.getSeverity() == ValidationEvent.FATAL_ERROR ||  ve.getSeverity() == ValidationEvent.ERROR){
    [javac]                                     ^
    [javac]   symbol:   variable ValidationEvent
    [javac]   location: class MyValidationEventHandler
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:36: error: cannot find symbol
    [javac]             if (ve.getSeverity() == ValidationEvent.FATAL_ERROR ||  ve.getSeverity() == ValidationEvent.ERROR){
    [javac]                                                                                         ^
    [javac]   symbol:   variable ValidationEvent
    [javac]   location: class MyValidationEventHandler
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java:37: error: cannot find symbol
    [javac]                     ValidationEventLocator  locator = ve.getLocator();
    [javac]                     ^
    [javac]   symbol:   class ValidationEventLocator
    [javac]   location: class MyValidationEventHandler
    [javac] /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java:36: error: method does not override or implement a method from a supertype
    [javac]     @Override
    [javac]     ^
    [javac] 83 errors

BUILD FAILED
/build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml:93: Compile failed; see the compiler error output for details.


Any hint how this can be fixed?

Kind regards

      Andreas.


[1] https://salsa.debian.org/med-team/biojava4-live

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