Importing sun.misc.Unsafe in bundle app

[vincenzo bonnici]

Hello.

I'm developing a Cytoscape3 bundle app which uses an external package that imports sun.misc.Unsafe.

Probably the dependence is due to the google concurrent hashmap package.

I'm testing it on Cytoscape 3.1.1.

For linux version, I just added this directive to the Cytoscape.vmoptions  file

-Dorg.osgi.framework.bootdelegation=sun.misc

and it works if a launch both commands ./cytoscape.sh and ./Cytoscape.

On a MAC machine, I was not so lucky.

It works only when I run ./cytoscape.sh but it does not work when I launch ./Cytoscape.app.

Any suggestion?

Thank you a lot.

Vincenzo

[Samad Lotia]

Hi Vincenzo,

I think this might be a problem with your Maven pom.xml file. The sun.misc.Unsafe class is part of the Oracle JVM and doesn't need to be imported by your bundle. What you'll need to do is include the sun.misc package as part of the Private-Package option to the Maven bundle plugin. Here's how that would look in your pom.xml file:

  ...
  <build>
    <plugins>
      <plugin>
        <groupId>org.apache.felix</groupId>
        <artifactId>maven-bundle-plugin</artifactId>
        <version>2.3.4</version>
        <extensions>true</extensions>
        <configuration>
          <instructions>
            <Bundle-SymbolicName>${bundle.pkg}</Bundle-SymbolicName>
            <Bundle-Name>Your bundle name</Bundle-Name>
            <Bundle-Version>${project.version}</Bundle-Version>
            <Export-Package>!${bundle.pkg}.internal.*</Export-Package>
            <Private-Package>${bundle.pkg}.*,sun.misc.*</Private-Package>
            <Bundle-Activator>${bundle.pkg}.internal.CyActivator</Bundle-Activator>
          </instructions>
        </configuration>
      </plugin>

Hope that helps,
Samad

[vincenzo bonnici]

Thank you a lot.

But it sill doesn't work.

That's what I get when I run my app from cytoscape.sh and removing the vmoption

Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: sun/misc/Unsafe

at com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.getUnsafe(ConcurrentHashMapV8.java:4136)

at com.googlecode.concurrentlinkedhashmap.ConcurrentHashMapV8.<clinit>(ConcurrentHashMapV8.java:4101)

at com.googlecode.concurrentlinkedhashmap.ConcurrentLinkedHashMap.<init>(ConcurrentLinkedHashMap.java:221)

at com.googlecode.concurrentlinkedhashmap.ConcurrentLinkedHashMap.<init>(ConcurrentLinkedHashMap.java:104)

at com.googlecode.concurrentlinkedhashmap.ConcurrentLinkedHashMap$Builder.build(ConcurrentLinkedHashMap.java:1634)

at com.orientechnologies.orient.core.db.record.ridbag.sbtree.OSBTreeCollectionManagerAbstract.<init>(OSBTreeCollectionManagerAbstract.java:22)

at com.orientechnologies.orient.core.db.record.ridbag.sbtree.OSBTreeCollectionManagerAbstract.<init>(OSBTreeCollectionManagerAbstract.java:28)

at com.orientechnologies.orient.client.remote.OSBTreeCollectionManagerRemote.<init>(OSBTreeCollectionManagerRemote.java:39)

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

at java.lang.reflect.Constructor.newInstance(Constructor.java:526)

at java.lang.Class.newInstance(Class.java:374)

at com.orientechnologies.orient.core.db.record.ODatabaseRecordAbstract$1.call(ODatabaseRecordAbstract.java:281)

at com.orientechnologies.orient.core.db.record.ODatabaseRecordAbstract$1.call(ODatabaseRecordAbstract.java:272)

at com.orientechnologies.common.concur.resource.OSharedContainerImpl.getResource(OSharedContainerImpl.java:53)

at com.orientechnologies.orient.client.remote.OStorageRemoteThread.getResource(OStorageRemoteThread.java:706)

at com.orientechnologies.orient.core.db.record.ODatabaseRecordAbstract.open(ODatabaseRecordAbstract.java:271)

at com.orientechnologies.orient.core.db.ODatabaseWrapperAbstract.open(ODatabaseWrapperAbstract.java:49)

at com.tinkerpop.blueprints.impls.orient.OrientBaseGraph.openOrCreate(OrientBaseGraph.java:1741)

at com.tinkerpop.blueprints.impls.orient.OrientBaseGraph.<init>(OrientBaseGraph.java:136)

at com.tinkerpop.blueprints.impls.orient.OrientTransactionalGraph.<init>(OrientTransactionalGraph.java:63)

at com.tinkerpop.blueprints.impls.orient.OrientTransactionalGraph.<init>(OrientTransactionalGraph.java:59)

at com.tinkerpop.blueprints.impls.orient.OrientGraph.<init>(OrientGraph.java:78)

[Samad Lotia]

Hi Vincezo,

Please tell me the JVM version you're using. You can find out by running "java -version" in the command prompt.

Thanks,

Samad

--
You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/Xdki5wxq7CU/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[vincenzo bonnici]

Hi Samad.

This is the output of update-alternatives

  Selection    Path                                            Priority   Status

------------------------------------------------------------

  0            /usr/lib/jvm/java-8-oracle/jre/bin/java          1090      auto mode

  1            /opt/java32/jre1.7.0_11/bin/java                 10        manual mode

  2            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode

* 3            /usr/lib/jvm/java-7-oracle/jre/bin/java          1089      manual mode

  4            /usr/lib/jvm/java-8-oracle/jre/bin/java          1090      manual mode

[vincenzo bonnici]

I also noted this warning during the maven build

[WARNING] Bundle mygroupid:myartifact:bundle:0.0.1-SNAPSHOT : Unused Private-Package instructions, no such package(s) on the class path: [sun.misc.*]

I'm doing it in Eclipse

[vincenzo bonnici]

If it could help

this is my pom file

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

<modelVersion>4.0.0</modelVersion>

<properties>

<bundle.symbolicName>mygroupid.myartifact</bundle.symbolicName>

<bundle.namespace>mygroupid.myartifact</bundle.namespace>

<bundle.Name>myArtifact</bundle.Name>

<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

<cytoscape.version>3.0.0</cytoscape.version>

<osgi.api.version>4.2.0</osgi.api.version>

<maven-enforcer-plugin>1.2</maven-enforcer-plugin>

<maven.version.range>[3.0.0,3.1.0)</maven.version.range>

<java.version>1.6</java.version>

</properties>

<groupId>mygroupid</groupId>

<artifactId>myartifact</artifactId>

<version>0.0.1-SNAPSHOT</version>

<name>${bundle.Name}</name>

<build>

<!-- 

<resources>

<resource>

<directory>src/main/resources</directory>

</resource>

</resources>

-->

<!-- Cytoscape requires Java 1.6 -->

<plugins>

<!-- Generates the OSGi metadata based on the osgi.bnd file. -->

<plugin>

<groupId>org.apache.felix</groupId>

<artifactId>maven-bundle-plugin</artifactId>

<version>2.5.3</version>

<extensions>true</extensions>

<configuration>

<instructions>

<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>

<Bundle-Version>${project.version}</Bundle-Version>

<Export-Package>${bundle.namespace}</Export-Package>

<Private-Package>${bundle.namespace}.internal.*</Private-Package>

<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>

<Embed-Dependency>*;scope=runtime|compile;optional=false</Embed-Dependency>

<Embed-Transitive>true</Embed-Transitive>

<Import-Package>*;resolution:=optional</Import-Package>

<Private-Package>${bundle.namespace}.*,sun.misc.*</Private-Package>

<!--

<Private-Package>${bundle.namespace}.*,sun.misc.*</Private-Package>

<Embed-Dependency>*;scope=runtime|compile;optional=false</Embed-Dependency>

<Embed-Transitive>true</Embed-Transitive>

<Import-Package>*;resolution:=optional</Import-Package>

-->

</instructions>

</configuration>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-compiler-plugin</artifactId>

<version>3.0</version>

<configuration>

<source>${java.version}</source>

<target>${java.version}</target>

<optimize>true</optimize>

</configuration>

</plugin>

<plugin>

<groupId>org.apache.maven.plugins</groupId>

<artifactId>maven-enforcer-plugin</artifactId>

<version>${maven-enforcer-plugin}</version>

<executions>

<execution>

<id>enforce-banned-dependencies</id>

<goals>

<goal>enforce</goal>

</goals>

<configuration>

<rules>

<bannedDependencies>

<searchTransitive>true</searchTransitive>

<excludes>

<exclude>javassist:javassist</exclude>

<!-- <exclude>commons-logging</exclude> -->

<exclude>aspectj:aspectj*</exclude> 

<exclude>hsqldb:hsqldb</exclude>

<exclude>log4j:log4j</exclude>

<exclude>org.slf4j:1.5*</exclude>

<exclude>org.springframework:2.*</exclude>

<exclude>org.springframework:3.0.*</exclude>

<exclude>javax.xml.bind:*</exclude>

<exclude>com.sun.xml.bind:*</exclude>

 

</excludes>

</bannedDependencies>

<requireMavenVersion>

<version>${maven.version.range}</version>

</requireMavenVersion>

<requireJavaVersion>

<version>${java.version}</version>

</requireJavaVersion>

</rules>

<fail>true</fail>

</configuration>

</execution>

</executions>

</plugin>

 

 

<plugin>

<groupId>com.orientechnologies</groupId>

<artifactId>orient-commons</artifactId>

<version>1.7.9</version>

<configuration>

<instructions>

<Embed-Dependency>scope=compile|runtime;type=!pom</Embed-Dependency>

<Import-Package>*;resolution:=optional</Import-Package>

</instructions>

</configuration>

</plugin>

<plugin>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-core</artifactId>

<version>1.7.9</version>

<configuration>

<instructions>

<Embed-Dependency>scope=compile|runtime;type=!pom</Embed-Dependency>

<Import-Package>*;resolution:=optional</Import-Package>

</instructions>

</configuration>

</plugin>

<plugin>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-client</artifactId>

<version>1.7.9</version>

<configuration>

<instructions>

<Embed-Dependency>scope=compile|runtime;type=!pom</Embed-Dependency>

<Import-Package>*;resolution:=optional</Import-Package>

</instructions>

</configuration>

</plugin>

<plugin>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-graphdb</artifactId>

<version>1.7.9</version>

<configuration>

<instructions>

<Embed-Dependency>scope=compile|runtime;type=!pom</Embed-Dependency>

<Import-Package>*;resolution:=optional</Import-Package>

</instructions>

</configuration>

</plugin>

<plugin>

<groupId>com.googlecode.concurrentlinkedhashmap</groupId>

<artifactId>concurrentlinkedhashmap-lru</artifactId>

<version>1.4</version>

<configuration>

<instructions>

<Embed-Dependency>scope=compile|runtime;type=!pom</Embed-Dependency>

<Import-Package>*;resolution:=optional</Import-Package>

</instructions>

</configuration>

</plugin>

</plugins>

</build>

<!-- Links to the Cytoscape Maven repositories. -->

<repositories>

<repository>

<id>cytoscape_releases</id>

<snapshots>

<enabled>false</enabled>

</snapshots>

<releases>

<enabled>true</enabled>

</releases>

<name>Cytoscape Releases</name>

<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>

</repository>

<repository>

<id>cytoscape_thirdparty</id>

<snapshots>

<enabled>false</enabled>

</snapshots>

<releases>

<enabled>true</enabled>

</releases>

<name>Cytoscape Third Party</name>

<url>http://code.cytoscape.org/nexus/content/repositories/thirdparty/</url>

</repository>

</repositories>

<dependencyManagement>

<dependencies>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>layout-api</artifactId>

<version>${cytoscape.version}</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>swing-util-api</artifactId>

<version>${cytoscape.version}</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>swing-application-api</artifactId>

<version>${cytoscape.version}</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>vizmap-api</artifactId>

<version>${cytoscape.version}</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>webservice-swing-api</artifactId>

<version>${cytoscape.version}</version>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>service-api</artifactId>

<version>${cytoscape.version}</version>

</dependency>

<dependency>

<groupId>org.ops4j.pax.logging</groupId>

<artifactId>pax-logging-api</artifactId>

<version>[1.5.2,2.0.0)</version>

</dependency>

<dependency>

<groupId>cytoscape-temp</groupId>

<artifactId>woodstox-core-lgpl</artifactId>

<version>[4.0.5, 5.0.0)</version>

</dependency>

<dependency>

<groupId>org.osgi</groupId>

<artifactId>org.osgi.core</artifactId>

<version>${osgi.api.version}</version>

</dependency>

<dependency>

<groupId>org.slf4j</groupId>

<artifactId>jcl-over-slf4j</artifactId>

<version>${slf4j.version}</version>

</dependency>

<dependency>

<groupId>org.slf4j</groupId>

<artifactId>log4j-over-slf4j</artifactId>

<version>${slf4j.version}</version>

</dependency>

 

 

 

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orient-commons</artifactId>

<version>1.7.9</version>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-core</artifactId>

<version>1.7.9</version>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-client</artifactId>

<version>1.7.9</version>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-graphdb</artifactId>

<version>1.7.9</version>

</dependency>

<dependency>

<groupId>com.googlecode.concurrentlinkedhashmap</groupId>

<artifactId>concurrentlinkedhashmap-lru</artifactId>

<version>1.4</version>

</dependency>

</dependencies>

</dependencyManagement>

<!-- Dependencies needed to compile this project. -->

<dependencies>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>layout-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>swing-util-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>swing-application-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>vizmap-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>webservice-swing-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.cytoscape</groupId>

<artifactId>service-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.ops4j.pax.logging</groupId>

<artifactId>pax-logging-api</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>cytoscape-temp</groupId>

<artifactId>woodstox-core-lgpl</artifactId>

<scope>provided</scope>

</dependency>

<dependency>

<groupId>org.osgi</groupId>

<artifactId>org.osgi.core</artifactId>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orient-commons</artifactId>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-core</artifactId>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-client</artifactId>

</dependency>

<dependency>

<groupId>com.orientechnologies</groupId>

<artifactId>orientdb-graphdb</artifactId>

</dependency>

<dependency>

<groupId>com.googlecode.concurrentlinkedhashmap</groupId>

<artifactId>concurrentlinkedhashmap-lru</artifactId>

</dependency>

</dependencies>

<packaging>bundle</packaging>

</project>

and this is the code who causes the crash

package mygroupid.myartifact.internal;

import java.awt.event.ActionEvent;

import javax.swing.JOptionPane;

import org.cytoscape.application.CyApplicationManager;

import org.cytoscape.application.swing.AbstractCyAction;

import com.tinkerpop.blueprints.impls.orient.OrientBaseGraph;

import com.tinkerpop.blueprints.impls.orient.OrientGraph;

//import sun.misc.Unsafe;

/**

 * Creates a new menu item under Apps menu section.

 *

 */

public class MenuAction extends AbstractCyAction {

public MenuAction(CyApplicationManager cyApplicationManager, final String menuTitle) {

super(menuTitle, cyApplicationManager, null, null);

setPreferredMenu("Apps");

}

public void actionPerformed(ActionEvent e) {

// Write your own function here.

JOptionPane.showMessageDialog(null, "Hello Cytoscape World!");

try{

OrientBaseGraph graph = new OrientGraph("remote:ncrnadb.scienze.univr.it/ncrnadb", "reader", "reader");

}catch(Exception ex){

ex.printStackTrace();

}

}

}

Thank you.

[Samad Lotia]

Hi Vincenzo,

When you build your bundle jar, could you unzip it and post the contents of META-INF/MANIFEST.MF file? This file may (or may not) be telling OSGi to try to import the sun.misc package.

Thanks,
Samad

--

[vincenzo bonnici]

Of course.

This is the manifest:

Manifest-Version: 1.0

Bnd-LastModified: 1413546127722

Build-Jdk: 1.7.0_67

Built-By: vbonnici

Bundle-Activator: mygroupid.myartifact.internal.CyActivator

Bundle-ClassPath: .,org.osgi.core-4.2.0.jar,orient-commons-1.7.9.jar,ori

 entdb-core-1.7.9.jar,orientdb-nativeos-1.7.9.jar,jna-4.0.0.jar,jna-plat

 form-4.0.0.jar,snappy-java-1.1.0.1.jar,orientdb-client-1.7.9.jar,orient

 db-enterprise-1.7.9.jar,orientdb-graphdb-1.7.9.jar,orientdb-server-1.7.

 9.jar,mail-1.4.jar,activation-1.1.jar,orientdb-tools-1.7.9.jar,orientdb

 -object-1.7.9.jar,hibernate-jpa-2.0-api-1.0.0.Final.jar,javassist-3.16.

 1-GA.jar,blueprints-core-2.5.0.jar,jettison-1.3.3.jar,stax-api-1.0.1.ja

 r,jackson-datatype-json-org-2.2.3.jar,jackson-core-2.2.2.jar,jackson-da

 tabind-2.2.2.jar,jackson-annotations-2.2.2.jar,json-20090211.jar,colt-1

 .2.0.jar,concurrent-1.3.4.jar,commons-configuration-1.6.jar,commons-col

 lections-3.2.1.jar,commons-lang-2.4.jar,commons-digester-1.8.jar,common

 s-beanutils-1.7.0.jar,commons-beanutils-core-1.8.0.jar,commons-logging-

 1.1.1.jar,pipes-2.5.0.jar,gremlin-java-2.5.0.jar,gremlin-groovy-2.5.0.j

 ar,ivy-2.3.0.jar,groovy-1.8.9.jar,antlr-2.7.7.jar,asm-3.2.jar,asm-commo

 ns-3.2.jar,asm-util-3.2.jar,asm-analysis-3.2.jar,asm-tree-3.2.jar,ant-1

 .8.3.jar,ant-launcher-1.8.3.jar,jansi-1.5.jar,jline-0.9.94.jar,concurre

 ntlinkedhashmap-lru-1.4.jar

Bundle-ManifestVersion: 2

Bundle-Name: myArtifact

Bundle-SymbolicName: mygroupid.myartifact

Bundle-Version: 0.0.1.SNAPSHOT

Created-By: Apache Maven Bundle Plugin

Embed-Dependency: *;scope=runtime|compile;optional=false

Embed-Transitive: true

Embedded-Artifacts: org.osgi.core-4.2.0.jar;g="org.osgi";a="org.osgi.cor

 e";v="4.2.0",orient-commons-1.7.9.jar;g="com.orientechnologies";a="orie

 nt-commons";v="1.7.9",orientdb-core-1.7.9.jar;g="com.orientechnologies"

 ;a="orientdb-core";v="1.7.9",orientdb-nativeos-1.7.9.jar;g="com.oriente

 chnologies";a="orientdb-nativeos";v="1.7.9",jna-4.0.0.jar;g="net.java.d

 ev.jna";a="jna";v="4.0.0",jna-platform-4.0.0.jar;g="net.java.dev.jna";a

 ="jna-platform";v="4.0.0",snappy-java-1.1.0.1.jar;g="org.xerial.snappy"

 ;a="snappy-java";v="1.1.0.1",orientdb-client-1.7.9.jar;g="com.orientech

 nologies";a="orientdb-client";v="1.7.9",orientdb-enterprise-1.7.9.jar;g

 ="com.orientechnologies";a="orientdb-enterprise";v="1.7.9",orientdb-gra

 phdb-1.7.9.jar;g="com.orientechnologies";a="orientdb-graphdb";v="1.7.9"

 ,orientdb-server-1.7.9.jar;g="com.orientechnologies";a="orientdb-server

 ";v="1.7.9",mail-1.4.jar;g="javax.mail";a="mail";v="1.4",activation-1.1

 .jar;g="javax.activation";a="activation";v="1.1",orientdb-tools-1.7.9.j

 ar;g="com.orientechnologies";a="orientdb-tools";v="1.7.9",orientdb-obje

 ct-1.7.9.jar;g="com.orientechnologies";a="orientdb-object";v="1.7.9",hi

 bernate-jpa-2.0-api-1.0.0.Final.jar;g="org.hibernate.javax.persistence"

 ;a="hibernate-jpa-2.0-api";v="1.0.0.Final",javassist-3.16.1-GA.jar;g="o

 rg.javassist";a="javassist";v="3.16.1-GA",blueprints-core-2.5.0.jar;g="

 com.tinkerpop.blueprints";a="blueprints-core";v="2.5.0",jettison-1.3.3.

 jar;g="org.codehaus.jettison";a="jettison";v="1.3.3",stax-api-1.0.1.jar

 ;g="stax";a="stax-api";v="1.0.1",jackson-datatype-json-org-2.2.3.jar;g=

 "com.fasterxml.jackson.datatype";a="jackson-datatype-json-org";v="2.2.3

 ",jackson-core-2.2.2.jar;g="com.fasterxml.jackson.core";a="jackson-core

 ";v="2.2.2",jackson-databind-2.2.2.jar;g="com.fasterxml.jackson.core";a

 ="jackson-databind";v="2.2.2",jackson-annotations-2.2.2.jar;g="com.fast

 erxml.jackson.core";a="jackson-annotations";v="2.2.2",json-20090211.jar

 ;g="org.json";a="json";v="20090211",colt-1.2.0.jar;g="colt";a="colt";v=

 "1.2.0",concurrent-1.3.4.jar;g="concurrent";a="concurrent";v="1.3.4",co

 mmons-configuration-1.6.jar;g="commons-configuration";a="commons-config

 uration";v="1.6",commons-collections-3.2.1.jar;g="commons-collections";

 a="commons-collections";v="3.2.1",commons-lang-2.4.jar;g="commons-lang"

 ;a="commons-lang";v="2.4",commons-digester-1.8.jar;g="commons-digester"

 ;a="commons-digester";v="1.8",commons-beanutils-1.7.0.jar;g="commons-be

 anutils";a="commons-beanutils";v="1.7.0",commons-beanutils-core-1.8.0.j

 ar;g="commons-beanutils";a="commons-beanutils-core";v="1.8.0",commons-l

 ogging-1.1.1.jar;g="commons-logging";a="commons-logging";v="1.1.1",pipe

 s-2.5.0.jar;g="com.tinkerpop";a="pipes";v="2.5.0",gremlin-java-2.5.0.ja

 r;g="com.tinkerpop.gremlin";a="gremlin-java";v="2.5.0",gremlin-groovy-2

 .5.0.jar;g="com.tinkerpop.gremlin";a="gremlin-groovy";v="2.5.0",ivy-2.3

 .0.jar;g="org.apache.ivy";a="ivy";v="2.3.0",groovy-1.8.9.jar;g="org.cod

 ehaus.groovy";a="groovy";v="1.8.9",antlr-2.7.7.jar;g="antlr";a="antlr";

 v="2.7.7",asm-3.2.jar;g="asm";a="asm";v="3.2",asm-commons-3.2.jar;g="as

 m";a="asm-commons";v="3.2",asm-util-3.2.jar;g="asm";a="asm-util";v="3.2

 ",asm-analysis-3.2.jar;g="asm";a="asm-analysis";v="3.2",asm-tree-3.2.ja

 r;g="asm";a="asm-tree";v="3.2",ant-1.8.3.jar;g="org.apache.ant";a="ant"

 ;v="1.8.3",ant-launcher-1.8.3.jar;g="org.apache.ant";a="ant-launcher";v

 ="1.8.3",jansi-1.5.jar;g="org.fusesource.jansi";a="jansi";v="1.5",jline

 -0.9.94.jar;g="jline";a="jline";v="0.9.94",concurrentlinkedhashmap-lru-

 1.4.jar;g="com.googlecode.concurrentlinkedhashmap";a="concurrentlinkedh

 ashmap-lru";v="1.4"

Export-Package: mygroupid.myartifact;version="0.0.1.SNAPSHOT"

Import-Package: com.jcraft.jsch;resolution:=optional,com.sun.jdi;resolut

 ion:=optional,com.sun.jdi.connect;resolution:=optional,com.sun.jdi.even

 t;resolution:=optional,com.sun.jdi.request;resolution:=optional,com.sun

 .tools.apt;resolution:=optional,com.sun.tools.javac;resolution:=optiona

 l,com.sun.tools.javah;resolution:=optional,com.sun.tools.javah.oldjavah

 ;resolution:=optional,com.thoughtworks.xstream;resolution:=optional,com

 .tinkerpop.blueprints.impls.sail;resolution:=optional,com.tinkerpop.rex

 ster.config;resolution:=optional,gnu.gcj;resolution:=optional,javax.acc

 essibility;resolution:=optional,javax.crypto;resolution:=optional,javax

 .crypto.spec;resolution:=optional,javax.imageio.spi;resolution:=optiona

 l,javax.management;resolution:=optional,javax.management.modelmbean;res

 olution:=optional,javax.management.remote;resolution:=optional,javax.ma

 nagement.remote.rmi;resolution:=optional,javax.management.timer;resolut

 ion:=optional,javax.naming;resolution:=optional,javax.naming.directory;

 resolution:=optional,javax.net;resolution:=optional,javax.net.ssl;resol

 ution:=optional,javax.print.attribute.standard;resolution:=optional,jav

 ax.rmi.ssl;resolution:=optional,javax.script;resolution:=optional,javax

 .security.auth.callback;resolution:=optional,javax.security.auth.x500;r

 esolution:=optional,javax.security.sasl;resolution:=optional,javax.serv

 let;resolution:=optional,javax.servlet.http;resolution:=optional,javax.

 servlet.jsp;resolution:=optional,javax.sql;resolution:=optional,javax.s

 wing;resolution:=optional,javax.swing.border;resolution:=optional,javax

 .swing.event;resolution:=optional,javax.swing.filechooser;resolution:=o

 ptional,javax.swing.plaf;resolution:=optional,javax.swing.plaf.metal;re

 solution:=optional,javax.swing.table;resolution:=optional,javax.swing.t

 ext;resolution:=optional,javax.swing.text.html;resolution:=optional,jav

 ax.swing.tree;resolution:=optional,javax.swing.undo;resolution:=optiona

 l,javax.xml.bind;resolution:=optional,javax.xml.bind.annotation;resolut

 ion:=optional,javax.xml.datatype;resolution:=optional,javax.xml.parsers

 ;resolution:=optional,javax.xml.transform;resolution:=optional,javax.xm

 l.transform.dom;resolution:=optional,javax.xml.transform.sax;resolution

 :=optional,javax.xml.transform.stream;resolution:=optional,javax.xml.va

 lidation;resolution:=optional,javax.xml.xpath;resolution:=optional,juni

 t.framework;resolution:=optional,junit.textui;resolution:=optional,kaff

 e.util;resolution:=optional,org.apache.avalon.framework.logger;resoluti

 on:=optional;version="[4.3,5)",org.apache.bsf;resolution:=optional,org.

 apache.bsf.util;resolution:=optional,org.apache.commons.cli;resolution:

 =optional,org.apache.commons.codec.binary;resolution:=optional,org.apac

 he.commons.httpclient;resolution:=optional,org.apache.commons.httpclien

 t.auth;resolution:=optional,org.apache.commons.httpclient.methods;resol

 ution:=optional,org.apache.commons.httpclient.params;resolution:=option

 al,org.apache.commons.jxpath;resolution:=optional,org.apache.commons.jx

 path.ri;resolution:=optional,org.apache.commons.jxpath.ri.compiler;reso

 lution:=optional,org.apache.commons.jxpath.ri.model;resolution:=optiona

 l,org.apache.commons.vfs;resolution:=optional,org.apache.commons.vfs.im

 pl;resolution:=optional,org.apache.env;resolution:=optional,org.apache.

 harmony.luni.util;resolution:=optional,org.apache.log;resolution:=optio

 nal,org.apache.log4j;resolution:=optional;version="[1.2,2)",org.apache.

 oro.text;resolution:=optional,org.apache.oro.text.regex;resolution:=opt

 ional,org.bouncycastle.bcpg;resolution:=optional,org.bouncycastle.jce.p

 rovider;resolution:=optional,org.bouncycastle.openpgp;resolution:=optio

 nal,org.cytoscape.application;resolution:=optional,org.cytoscape.applic

 ation.swing;resolution:=optional;version="[3.0,4)",org.cytoscape.servic

 e.util;resolution:=optional;version="[3.0,4)",org.cytoscape.view.model;

 resolution:=optional;version="[3.0,4)",org.junit;resolution:=optional,o

 rg.w3c.dom;resolution:=optional,org.w3c.dom.bootstrap;resolution:=optio

 nal,org.w3c.dom.ls;resolution:=optional,org.xml.sax;resolution:=optiona

 l,org.xml.sax.ext;resolution:=optional,org.xml.sax.helpers;resolution:=

 optional,sun.awt;resolution:=optional,sun.java2d.pipe;resolution:=optio

 nal,sun.misc;resolution:=optional,sun.rmi.rmic;resolution:=optional,sun

 .tools.javac;resolution:=optional,sun.tools.native2ascii;resolution:=op

 tional,weblogic;resolution:=optional

Require-Capability: osgi.ee;filter:="(&(osgi.ee=JavaSE)(version=1.6))"

Tool: Bnd-2.3.0.201405100607

[vincenzo bonnici]

By the way, is it normal that it is including (copying) all the needed packages (the Bundle-ClassPath list) inside the package?

[Samad Lotia]

I can't figure out why Maven is insisting on importing the sun.misc package when it is provided by the JRE. I searched for the answer for resolving the sun.misc issue, and it looks like your original solution of changing the line in Cytoscape.vmoptions is the only one I could find.

I discussed this issue with other Cytoscape core developers, and as of right now we can't distribute Cytoscape with the modifications you made to the Cytoscape.vmoptions file. However, we would still encourage you to distribute your app with instructions on modifying the vmoptions file to include the sun.misc package.

I apologize for not being enough help!

On Fri, Oct 17, 2014 at 4:47 AM, vincenzo bonnici <vincenzo...@gmail.com> wrote:

By the way, is it normal that it is including (copying) all the needed packages (the Bundle-ClassPath list) inside the package?

--

[vincenzo bonnici]

No worries.

Thank you a lot! :)