Your message dated Thu, 3 Nov 2022 22:41:34 +0100
with message-id <a02a6711-d40e-8569-3e80-0172d31d1...@debian.org>
and subject line Closing bug 1011977 : htsjdk builds against OpenJDK17
has caused the Debian Bug report #1011977,
regarding FTBFS with OpenJDK 17: 5 failing tests
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1011977: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1011977
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: htsjdk
Version: 2.24.1+dfsg-3
Severity: important
Tags: ftbfs sid bookworm
User: debian-j...@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
--- End Message ---
--- Begin Message ---
Version: 3.0.2+dfsg-1~exp0
Hello,
The bug has been fixed is the version that is currently in experimental,
I have just made an upload to unstable and it also built successfully
against OpenJDK17.
Cheers,
--
Pierre
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--- End Message ---
