[Debian-med-packaging] Help for package sepp needed: error: incompatible types: JSONArray cannot be converted to Collection<? extends JSONArray>

[Andreas Tille]

Hi,

the Debian Med team wants to package sepp[1] as a COVID-19 relevant
package.  It contains some Java code which fails to build with:

...
    [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.
    [javac] /build/sepp-4.3.10+dfsg/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Trees.java:32: warning: SunGraphicsEnvironment is internal proprietary API and may be removed in a future release
    [javac] import sun.java2d.SunGraphicsEnvironment;
    [javac]                  ^
    [javac] /build/sepp-4.3.10+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:391: error: incompatible types: JSONArray cannot be converted to Collection<? extends JSONArray>
    [javac]         sortedPlacements.addAll(placements);
    [javac]                                 ^
    [javac] /build/sepp-4.3.10+dfsg/tools/merge/src/phylolab/taxonamic/JSONMerger.java:562: error: incompatible types: JSONArray cannot be converted to Collection<? extends JSONObject>
    [javac]       sortedPlacements.addAll(resultsPlacements);
    [javac]                               ^
    [javac] /build/sepp-4.3.10+dfsg/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java:315: error: incompatible types: JSONArray cannot be converted to Collection<? extends JSONObject>
    [javac]                         sortedPlacements.addAll(resultsPlacements);
    [javac]                                                 ^
    [javac] Note: Some input files use or override a deprecated API.
...


Any help for the "incompatible types" types issue?  I'm also wondering
how serious I should take the "SunGraphicsEnvironment is internal
proprietary API" issue.

Kind regards

         Andreas.


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

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