[Debian-med-packaging] Bug#1011977: FTBFS with OpenJDK 17: 5 failing tests

[Pierre Gruet]

Source: htsjdk
Version: 2.24.1+dfsg-3
Severity: important
Tags: ftbfs sid bookworm
User: debian-java at lists.debian.org
Usertags: default-java17

htsjdk fails to build with OpenJDK 17, the jar can be built but then 5 tests
fail, although all of them pass with OpenJDK 11:


 Gradle suite > Gradle test > htsjdk.samtools.fastq.BasicFastqWriterTest.testFlushNotSpammed FAILED
     java.lang.AssertionError: expected [true] but found [false]
         at org.testng.Assert.fail(Assert.java:94)
         at org.testng.Assert.failNotEquals(Assert.java:513)
         at org.testng.Assert.assertTrue(Assert.java:42)
         at org.testng.Assert.assertTrue(Assert.java:52)
         at htsjdk.samtools.fastq.BasicFastqWriterTest.testFlushNotSpammed(BasicFastqWriterTest.java:41)

 Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[0](unsorted.sam, samFilter01.js, 8) FAILED
     htsjdk.samtools.util.RuntimeScriptException: The embedded 'javascript' engine is not available in java. Do you use the SUN/Oracle Java Runtime ?
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:90)
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:65)
         at htsjdk.samtools.filter.JavascriptSamRecordFilter.<init>(JavascriptSamRecordFilter.java:58)
         at htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters(JavascriptSamRecordFilterTest.java:58)
 
 Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[1](unsorted.sam, samFilter02.js, 10) FAILED
     htsjdk.samtools.util.RuntimeScriptException: The embedded 'javascript' engine is not available in java. Do you use the SUN/Oracle Java Runtime ?
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:90)
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:65)
         at htsjdk.samtools.filter.JavascriptSamRecordFilter.<init>(JavascriptSamRecordFilter.java:58)
         at htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters(JavascriptSamRecordFilterTest.java:58)
 
 Gradle suite > Gradle test > htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters[0](ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf, variantFi     lter01.js, 61) FAILED
     htsjdk.samtools.util.RuntimeScriptException: The embedded 'javascript' engine is not available in java. Do you use the SUN/Oracle Java Runtime ?
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:90)
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:65)
         at htsjdk.variant.variantcontext.filter.JavascriptVariantFilter.<init>(JavascriptVariantFilter.java:54)
         at htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters(JavascriptVariantFilterTest.java:57)
 
 Gradle suite > Gradle test > htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters[1](ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf, variantFi     lter02.js, 38) FAILED
     htsjdk.samtools.util.RuntimeScriptException: The embedded 'javascript' engine is not available in java. Do you use the SUN/Oracle Java Runtime ?
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:90)
         at htsjdk.samtools.filter.AbstractJavascriptFilter.<init>(AbstractJavascriptFilter.java:65)
         at htsjdk.variant.variantcontext.filter.JavascriptVariantFilter.<init>(JavascriptVariantFilter.java:54)
         at htsjdk.variant.variantcontext.filter.JavascriptVariantFilterTest.testJavascriptFilters(JavascriptVariantFilterTest.java:57)


Best,

-- 
Pierre