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Test on Java 11 #106

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merged 4 commits into from
Jul 2, 2019
Merged

Test on Java 11 #106

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116c923
Test on Java 11
tomwhite Jan 28, 2019
3a04064
NO_GCE_CHECK=true
tomwhite Jun 10, 2019
0f646f4
Revert "NO_GCE_CHECK=true"
tomwhite Jul 2, 2019
8b113bf
Global NO_GCE_CHECK=true
tomwhite Jul 2, 2019
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16 changes: 11 additions & 5 deletions .travis.yml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,18 @@
language: java
sudo: required
jdk:
- oraclejdk8
- openjdk8
matrix:
include:
- jdk: oraclejdk8
env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
- jdk: openjdk8
env: JAVA_RELEASE=8 JAVA_VERSION=1.8 SCALA_VERSION=2.11
- jdk: openjdk11
env: JAVA_RELEASE=11 JAVA_VERSION=11 SCALA_VERSION=2.12
env:
- NO_GCE_CHECK=true
global:
- NO_GCE_CHECK=true
script:
- mvn -B verify -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
- mvn -B verify -Djava.release=$JAVA_RELEASE -Djava.version=$JAVA_VERSION -Dscala.version=$SCALA_VERSION -Ddisq.test.real.world.files.dir=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large -Ddisq.test.real.world.files.ref=$TRAVIS_BUILD_DIR/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta -Ddisq.samtools.bin=/usr/bin/samtools -Ddisq.bcftools.bin=/usr/bin/bcftools
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I hate that it's sometimes 1.8 and sometimes 8, but what can you do...

cache:
directories:
- $HOME/.m2
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31 changes: 28 additions & 3 deletions pom.xml
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Expand Up @@ -30,15 +30,17 @@
</developers>

<properties>
<maven.compiler.target>1.8</maven.compiler.target>
<maven.compiler.source>1.8</maven.compiler.source>
<java.release>8</java.release>
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I assume that if you specify a property on the command line it automatically overrules the one that's included in the file?

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That's right

<java.version>1.8</java.version>
<maven.compiler.target>${java.version}</maven.compiler.target>
<maven.compiler.source>${java.version}</maven.compiler.source>
<htsjdk.version>2.19.0</htsjdk.version>
<hadoop.version>2.7.5</hadoop.version>
<mockito.version>2.22.0</mockito.version>
<kryo-serializers.version>0.42</kryo-serializers.version>
<slf4j.version>1.7.25</slf4j.version>
<scala.version>2.11</scala.version>
<spark.version>2.3.2</spark.version>
<spark.version>2.4.3</spark.version>
</properties>

<dependencies>
Expand Down Expand Up @@ -161,6 +163,11 @@

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
Expand Down Expand Up @@ -338,6 +345,24 @@
</distributionManagement>

<profiles>
<profile>
<id>java11</id>
<activation>
<jdk>11</jdk>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
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Dumb maven question: why do we need a java11 profile? to specify a different compiler plugin?

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It's to set the maven-compiler-plugin's release configuration property. Annoyingly this is not recognized by the Java 8 compiler, so it can only be set in the Java 11 configuration. Using a profile was the only way I could see to do this.

<version>3.8.0</version>
<configuration>
<release>${java.release}</release>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>release</id>
<build>
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15 changes: 15 additions & 0 deletions src/build/conf/spotbugs-exclude.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
<FindBugsFilter>
<Match>
<!-- Java 11 false positive -->
<!-- https://github.com/spotbugs/spotbugs/issues/756 -->
<Bug pattern="RCN_REDUNDANT_NULLCHECK_WOULD_HAVE_BEEN_A_NPE" />
</Match>
<Match>
<!-- Java 11 false positive -->
<!-- https://github.com/spotbugs/spotbugs/issues/756 -->
<Or>
<Bug pattern="NP_LOAD_OF_KNOWN_NULL_VALUE" />
<Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NONNULL_VALUE" />
<Bug pattern="RCN_REDUNDANT_NULLCHECK_OF_NULL_VALUE" />
</Or>
<Class name="org.disq_bio.disq.impl.formats.cram.CramSource"/>
</Match>
<Match>
<Class name="org.disq_bio.disq.impl.file.SeekableByteChannelPrefetcher"/>
</Match>
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