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Make biojava work with java 9, 10, 11 #805

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merged 7 commits into from
Sep 12, 2018
Merged

Make biojava work with java 9, 10, 11 #805

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c54f698
Make BioJava compile under java9
sbliven Jun 18, 2018
80316d7
Update travis JDK
sbliven Jun 20, 2018
84df99b
Update maven plugin versions.
sbliven Jun 20, 2018
ac45053
Explicit jaxb dependencies so that biojava can compile/run in all jdk…
josemduarte Sep 7, 2018
941b074
Keeping the java 8 compliance level (compiled byte code is 8).
josemduarte Sep 7, 2018
5255bc3
Reverting travis jre version to 8
josemduarte Sep 11, 2018
27c5fbb
Removing comment that doesn't apply anymore
josemduarte Sep 11, 2018
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3 changes: 0 additions & 3 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java
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Expand Up @@ -20,8 +20,6 @@
*/
package org.biojava.nbio.core.sequence.io.embl;

import jdk.nashorn.internal.ir.annotations.Immutable;

/**
* This class contains the processed data of embl file
* Primary accession number
Expand All @@ -35,7 +33,6 @@
* @author Noor Aldeen Al Mbaidin
* @since 5.0.0
*/
@Immutable
public class EmblId {


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4 changes: 4 additions & 0 deletions biojava-protein-disorder/pom.xml
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Expand Up @@ -84,6 +84,10 @@
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
</dependencies>

<properties>
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19 changes: 19 additions & 0 deletions biojava-structure/pom.xml
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Expand Up @@ -62,6 +62,25 @@
<version>1.1.0</version>
</dependency>

<!-- JAXb explicit dependency is needed since Java 9. See https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j
Note versions are set in parent pom in dependency management section -->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
</dependency>

<!-- logging dependencies (managed by parent pom, don't set versions or
scopes here) -->
<dependency>
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51 changes: 34 additions & 17 deletions pom.xml
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Expand Up @@ -32,6 +32,7 @@
</license>
</licenses>
<properties>
<!-- Notice: if using java 9 or 10 jres, it is possible to simply use here "8", "9" or "10". But if using java 8 jre, "8" is not an allowed value but only "1.8"-->
<jdk.version>1.8</jdk.version>
<maven.enforcer.jdk-version>1.8</maven.enforcer.jdk-version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
Expand Down Expand Up @@ -171,27 +172,23 @@
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.0.2</version>
<version>3.1.1</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<!-- warning: before upgrading to a newer version of this plugin
there are some config changes required.
see https://github.com/biojava/biojava/issues/531
-->
<version>3.0.2</version>
<version>3.1.0</version>
</plugin>
<plugin>
<artifactId>maven-scm-plugin</artifactId>
<version>1.9.5</version>
<version>1.10.0</version>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.1</version>
</plugin>
<plugin>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.21.0</version>
<version>2.22.0</version>
</plugin>
<plugin>
<groupId>net.sf</groupId>
Expand All @@ -201,7 +198,7 @@
<plugin>
<groupId>org.jvnet.jaxb2.maven2</groupId>
<artifactId>maven-jaxb2-plugin</artifactId>
<version>0.13.1</version>
<version>0.14.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
Expand All @@ -224,7 +221,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.0</version>
<version>3.0.1</version>
<configuration>
<additionalJOptions>-Xdoclint:none</additionalJOptions>
<!-- we need to allow script in comments or otherwise we can't use google analytics js in footer below - JD 2017-03-30 -->
Expand All @@ -242,7 +239,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<version>3.1.1</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
Expand Down Expand Up @@ -280,18 +277,18 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
<version>3.0.0</version>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<version>3.1.0</version>
</plugin>

<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.0.0-M1</version>
<version>3.0.0-M2</version>
<executions>
<execution>
<id>enforce-java</id>
Expand All @@ -316,12 +313,12 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.21.0</version>
<version>2.22.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.7</version>
<version>3.7.1</version>
</plugin>

</plugins>
Expand Down Expand Up @@ -507,6 +504,26 @@
<artifactId>forester</artifactId>
<version>1.038</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.0</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
<version>2.3.0</version>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.3.0</version>
</dependency>
<dependency>
<groupId>javax.activation</groupId>
<artifactId>activation</artifactId>
<version>1.1.1</version>
</dependency>
</dependencies>
</dependencyManagement>

Expand All @@ -518,7 +535,7 @@
<aggregate>true</aggregate>
<breakiterator>true</breakiterator>
<quiet>true</quiet>
<source>1.8</source>
<source>${jdk.version}</source>
<verbose>false</verbose>
<linksource>true</linksource>

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