Develop Reference

Sonarqube scan from Jenkins : ClassNotFoundException: org.eclipse.jgit.api.Git

I have a problem when doing a SonarQube Scan from Jenkins. See the stacktrace in debug mode :
[ERROR] Failed to execute goal org.sonarsource.scanner.maven:sonar-maven-plugin:3.2:sonar (default-cli) on project scbm-order-parent: Unable to register extension org.sonarsource.scm.git.JGitBlameCommand from plugin 'scmgit': org/eclipse/jgit/api/Git: org.eclipse.jgit.api.Git -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.sonarsource.scanner.maven:sonar-maven-plugin:3.2:sonar (default-cli) on project scbm-order-parent: Unable to register extension org.sonarsource.scm.git.JGitBlameCommand from plugin 'scmgit'
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:216)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:120)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:347)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:154)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:582)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:214)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:158)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Unable to register extension org.sonarsource.scm.git.JGitBlameCommand from plugin 'scmgit'
at org.sonarsource.scanner.maven.bootstrap.ExceptionHandling.handle(ExceptionHandling.java:36)
at org.sonarsource.scanner.maven.bootstrap.ScannerBootstrapper.execute(ScannerBootstrapper.java:81)
at org.sonarsource.scanner.maven.SonarQubeMojo.execute(SonarQubeMojo.java:122)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:132)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
... 19 more
Caused by: java.lang.IllegalStateException: Unable to register extension org.sonarsource.scm.git.JGitBlameCommand from plugin 'scmgit'
at org.sonar.core.platform.ComponentContainer.addExtension(ComponentContainer.java:249)
at org.sonar.scanner.bootstrap.ExtensionInstaller.doInstall(ExtensionInstaller.java:76)
at org.sonar.scanner.bootstrap.ExtensionInstaller.install(ExtensionInstaller.java:57)
at org.sonar.scanner.scan.ProjectScanContainer.addBatchExtensions(ProjectScanContainer.java:227)
at org.sonar.scanner.scan.ProjectScanContainer.doBeforeStart(ProjectScanContainer.java:115)
at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:141)
at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:128)
at org.sonar.scanner.task.ScanTask.execute(ScanTask.java:47)
at org.sonar.scanner.task.TaskContainer.doAfterStart(TaskContainer.java:86)
at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:143)
at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:128)
at org.sonar.scanner.bootstrap.GlobalContainer.executeTask(GlobalContainer.java:118)
at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:117)
at org.sonarsource.scanner.api.internal.batch.BatchIsolatedLauncher.execute(BatchIsolatedLauncher.java:62)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.sonarsource.scanner.api.internal.IsolatedLauncherProxy.invoke(IsolatedLauncherProxy.java:60)
at com.sun.proxy.$Proxy31.execute(Unknown Source)
at org.sonarsource.scanner.api.EmbeddedScanner.doExecute(EmbeddedScanner.java:233)
at org.sonarsource.scanner.api.EmbeddedScanner.runAnalysis(EmbeddedScanner.java:151)
at org.sonarsource.scanner.maven.bootstrap.ScannerBootstrapper.execute(ScannerBootstrapper.java:78)
... 22 more
Caused by: java.lang.NoClassDefFoundError: org/eclipse/jgit/api/Git
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
at java.lang.Class.getDeclaredMethods(Class.java:1975)
at org.picocontainer.injectors.AdaptingInjection$1.run(AdaptingInjection.java:203)
at java.security.AccessController.doPrivileged(Native Method)
at org.picocontainer.injectors.AdaptingInjection.injectionMethodAnnotated(AdaptingInjection.java:200)
at org.picocontainer.injectors.AdaptingInjection.methodAnnotatedInjectionAdapter(AdaptingInjection.java:171)
at org.picocontainer.injectors.AdaptingInjection.createComponentAdapter(AdaptingInjection.java:70)
at org.picocontainer.behaviors.AbstractBehaviorFactory.createComponentAdapter(AbstractBehaviorFactory.java:44)
at org.picocontainer.behaviors.OptInCaching.createComponentAdapter(OptInCaching.java:45)
at org.picocontainer.DefaultPicoContainer.addComponent(DefaultPicoContainer.java:536)
at org.picocontainer.DefaultPicoContainer.access$300(DefaultPicoContainer.java:84)
at org.picocontainer.DefaultPicoContainer$AsPropertiesPicoContainer.addComponent(DefaultPicoContainer.java:1149)
at org.sonar.core.platform.ComponentContainer.addExtension(ComponentContainer.java:247)
... 44 more
Caused by: java.lang.ClassNotFoundException: org.eclipse.jgit.api.Git
at org.sonar.classloader.ParentFirstStrategy.loadClass(ParentFirstStrategy.java:39)
at org.sonar.classloader.ClassRealm.loadClass(ClassRealm.java:87)
at org.sonar.classloader.ClassRealm.loadClass(ClassRealm.java:76)
... 58 more
Used versions :
Jenkins 1.624 (ok... old one but cannot upgrade it now)
sources scan with Java 8
Sonarqube 6.3 (Git plugin version 1.2, java plugin version 4.6.0.8784)
Extract from the pom.xml :
<pluginManagement>
<plugin>
<groupId>org.sonarsource.scanner.maven</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>3.2</version>
</plugin>
</pluginManagement>
mvn command line :
clean install -U -X org.sonarsource.scanner.maven:sonar-maven-plugin:3.2:sonar -Dsonar.host.url=http://x.x.x.x:9000 -Dsonar.working.directory=/tmp/.sonar/ -Dsonar.login=xxxxxxxxxxxxxx -DskipTests=true site
Any idea ?
I have also tried to add the JGit artifact in the plugin management part in my pom.xml, without success... :(

Ok, it works now. Just disable Git SCM plugin. Don't know why...
Then disable Sonar XML Plugin because of the next error :
Caused by: java.lang.ClassNotFoundException: org.sonar.squidbridge.api.AnalysisException
If anyone know why, please answer :)
I have also seen that some guys have updated JGit dependency version in Sonar Git plugin : https://groups.google.com/forum/#!topic/sonarqube/TcRrB9XBk8o.
Not tested...

We ran into a similar issue with Sonarqube v5.6.7. The root cause appears to have been that the local cache of the plugin library that gets downloaded by the sonar scanner was corrupted.
Content found under "/logs/ssc/sonar/cache/cache":
./675ef60911b1d93e17e84ab20261e18a
./675ef60911b1d93e17e84ab20261e18a/sonar-xml-plugin-1.5-SNAPSHOT.jar_unzip
./675ef60911b1d93e17e84ab20261e18a/sonar-xml-plugin-1.5-SNAPSHOT.jar_unzip/META-INF
./675ef60911b1d93e17e84ab20261e18a/sonar-xml-plugin-1.5-SNAPSHOT.jar_unzip/META-INF/lib
Note that the "lib" dir was empty. Deleting the entire content of the "/logs/ssc/sonar/cache/cache" cache directory and running another project scan caused it to re-download and the lib dir was now populated with the list of dependency libraries for that plugin.
To find where the local cache of plugin jars lived I ran "strace -f -e trace=open,close,read,write -o strace.log " and then searched "strace.log" for a plugin name.

Building Eclipse IDE from scratch - how to specify the target OS?

This post is about building the whole Eclipse IDE from the source code - and more in particular how to specify the target OS you want to build the executable for.
I found the following tutorial to guide me through the build procedure: http://www.vogella.com/tutorials/EclipsePlatformDevelopment/article.html
Especially chapter 13 of that Tutorial is helpful. I will describe the steps that need to be taken one by one here - so you don't need to read the vogella tutorial.
NEEDED SOFTWARE :
Apparently you need to have the following software installed on your (Windows) machine:
Git
Maven Version 3.3.1 (make sure that the bin folder where you extract Maven is added to the PATH. For installation instructions see https://maven.apache.org/install.html)
Oracle 1.8 JDK or higher (don't forget to set the JAVA_HOME environment variable)
Now you're ready to start:
STEP 1 :
Create a new folder in the C:\ disk. Let's name it C:\myEclipse. This will be the folder in which we pull the Git repository of the latest Eclipse version.
STEP 2 :
Open the Windows cmd shell with administrator privileges (right click on cmd icon if you made one on your desktop, and select open with admin rights). Go to that folder through the command cd C:\myEclipse. Now type the following command: git config --system core.longpaths true. This notifies Git that long names can occur in the repository. Forget this command and it will result in errors later on.
STEP 3 :
Clone the Git repository:
git clone -b master --recursive git://git.eclipse.org/gitroot/platform/eclipse.platform.releng.aggregator.git
Now you should have some patience for all the sourcecode to get copied to your local folder.
STEP 4 :
Finally it is time to start the build. The build procedure will already take hours, so it is wise to skip the unit tests. Therefore do not forget to add the -DskipTests parameter. This is the command to start the build:
mvn clean verify -DskipTests
After some hours, the build should be finished.
STEP 5 :
The results of the build should now be in the following folder:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.releng.tychoeclipsebuilder\sdk\target\products
Notice that the Eclipse IDE is built for all possible target machines. 32-bit Windows, 64-bit Windows, Macintosh, Linux, ... No wonder it takes hours! I would like to build for just one single target - for example my 64-bit Windows machine. This will hopefully reduce the build time significantly and allow me to verify code changes quicker.
Does anyone know how to achieve this?
EDIT :
I have added the argument -Dnative=win32.win32.x86_64 to the build command. Unfortunately, I get an error after 15 to 20 mins. This time, I've added the argument -X as well, to get debug information:
...
[INFO] equinox-sdk ........................................ SKIPPED
[INFO] org.eclipse.rcp.id ................................. SKIPPED
[INFO] org.eclipse.rcp.sdk.id ............................. SKIPPED
[INFO] org.eclipse.platform.ide ........................... SKIPPED
[INFO] org.eclipse.platform.sdk ........................... SKIPPED
[INFO] org.eclipse.sdk.ide ................................ SKIPPED
[INFO] eclipse-junit-tests ................................ SKIPPED
[INFO] eclipse.platform.repository ........................ SKIPPED
[INFO] platform-aggregator ................................ SKIPPED
[INFO] -----------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] -----------------------------------------------------------------------
[INFO] Total time: 23:54 min
[INFO] Finished at: 2016-06-19T18:12:14+02:00
[INFO] Final Memory: 668M/3263M
[INFO] -----------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:1.8: run (natives) on project org.eclipse.swt.win32.win32.x86_64: An Ant BuildException has occured: The following error occurred while executing this line:
[ERROR] C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:915: The following error occurred while executing this line:
[ERROR] C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:1012: exec returned: 1
[ERROR] around Ant part ...<ant antfile="build.xml" target="build_libraries"/>... # 4:54 in C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt.binaries\bundles\org.eclipse.swt.win32.win32.x86_64\target\antrun\build-main.xml
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:1.8:
run (natives) on project org.eclipse.swt.win32.win32.x86_64:
An Ant BuildException has occured:
The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:915: The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:1012: exec returned: 1 around Ant part ...<ant antfile="build.xml" target="build_libraries"/>... # 4:54 in C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt.binaries\bundles\org.eclipse.swt.win32.win32.x86_64\target\antrun\build-main.xml
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by:
org.apache.maven.plugin.MojoExecutionException:
An Ant BuildException has occured:
The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:915:
The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:1012: exec returned: 1 around Ant part ...<ant antfile="build.xml" target="build_libraries"/>... # 4:54 in C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt.binaries\bundles\org.eclipse.swt.win32.win32.x86_64\target\antrun\build-main.xml
at org.apache.maven.plugin.antrun.AntRunMojo.execute(AntRunMojo.java:342)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(Default BuildPluginManager.java:134)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
... 20 more
Caused by: C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt.binaries\bundles\org.eclipse.swt.win32.win32.x86_64\target\antrun\build-main.xml
:4: The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml
:915:The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:1012: exec returned: 1
at org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHelper.java:568)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:443)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor67.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
at org.apache.maven.plugin.antrun.AntRunMojo.execute(AntRunMojo.java:313)
... 22 more
Caused by: C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml
:915: The following error occurred while executing this line:
C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:1012: exec returned: 1
at org.apache.tools.ant.ProjectHelper.addLocationToBuildException(ProjectHelper.java:568)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:443)
at org.apache.tools.ant.taskdefs.CallTarget.execute(CallTarget.java:105)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor67.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
... 33 more
Caused by: C:\myEclipse\eclipse.platform.releng.aggregator\eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml:1012: exec returned: 1
at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:643)
at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:669)
at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:495)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor67.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
... 46 more
[ERROR]
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn <goals> -rf :org.eclipse.swt.win32.win32.x86_64
I still have no answer, so I started a bounty. Please reproduce step 1 until step 5 on your machine (with the -Dnative=win32.win32.x86_64 argument added to the fourth step). Do you achieve a successful build of the Eclipse IDE for just one OS target (preferably Windows 64-bit)? Does the build go faster - compared to the general build process that targets all OS's?
PS: I've got some other questions related to the Eclipse "Build from scratch" topic. If you're interested:
Building Eclipse IDE from scratch - how to choose CDT over JDT?
Building Eclipse IDE from scratch - how to specify the target OS?
Building Eclipse IDE from scratch - making bigger icons sometimes successful
Let us all unite to build the Eclipse IDE ourselves - and tweak it to our needs ;-)
EDIT :
Mr/Mss. Zapl wrote an interesting comment. He/She thinks that the -Dnative argument is not correct, after he/she read the following link:
http://comments.gmane.org/gmane.comp.ide.eclipse.cbi.devel/896
Hopefully we'll get closer to the answer now :-)
FINAL EDIT :
Suddenly this question catched the attention of the community. I got a lot of suggestions/answers in a short time. I cannot verify every single one of them right now because the build procedure takes about 2 hours.
I have 19 hours left to award the 50 points bounty. Please let me know if you successfully reproduced the STEPS 1..5 from this question on your own machine, and succeeded to build the Eclipse IDE from scratch for one specific OS. I will award you the bonus :-)

This snippet is taken from a working pom.xml that exports to win32.win32.x86_64.
Maybe some parts are not required for your project but it may be a good starting point to add this to your pom file.
..
..
<build>
<plugins>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-maven-plugin</artifactId>
<version>0.20.0</version>
<extensions>true</extensions>
</plugin>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>target-platform-configuration</artifactId>
<version>0.20.0</version>
<configuration>
<resolver>p2</resolver>
<environments>
<environment>
<os>win32</os>
<ws>win32</ws>
<arch>x86_64</arch>
</environment>
</environments>
</configuration>
</plugin>
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>tycho-compiler-plugin</artifactId>
<version>0.20.0</version>
<configuration>
<compilerArgument>-err:-forbidden</compilerArgument>
</configuration>
</plugin>
</plugins>
</build>
..
..
EDIT
As mentioned in the comments I followed your steps and had some problems. I solved most of them now. If someone else also gets a lot of errors here are some solutions.
In the file eclipse.pde.ui/pom.xml line 19: the version was 4.6.0-SNAPSHOT, but has to be 4.7.0-SNAPSHOT
Hint: To speed up the build you can add e.g. "-T 4" to the mvn command to enable parallel builds. I finally ended with >mvn clean verify -DSkipTests -T 4 -Dnative=win32.win32.x86_64
After this fix I was able to run until I got the same errors mentioned in the initial question.
I went to the project folder \eclipse.platform.swt.binaries\bundles\org.eclipse.swt.win32.win32.x86_64 and started an Ant build (Apache Ant version 1.9.7) and it finished without errors. But I got the same errors when it was executed by the Maven build.
Thus, I checked lines 915 and 1012 of the file \eclipse.platform.swt\bundles\org.eclipse.swt\buildSWT.xml. After setting failonerror="false" (is set to "true" by default) in both lines I was able to continue with the build. I assess this as a very poor solution and it should not be the final solution for a problem to disable such tests.
Finally, I ended with errors in project org.eclipse.pde.build.tests and stopped following the problems.
The whole project seems to be misconfigured in many parts and I could not find a better solution so far. People should remember the golden rule not to commit anything that breaks the build to avoid such problems. Maybe the problems will be solved after a few updates to the repo.

There are multiple projects that are built here
SWT natives. (-Dnative=)
IDE. (platform independent)
SWT natives are built(by SWT team) every day at 19:00 EST/EDT everyday and pushed to eclipse.platform.swt.binaries.git repo. This build requires a quite a bit of dependencies like visual studio, xulrunner, WebKit, etc. For trying out a build I don't suggest you to attempt this .
CBI(Common Build Infrastructure) does the eclipse plugin builds and signing and packaging. This process is platform independent.
CBI build starts at 20:00 EST/EDT daily and the swt.binaries are picked up only during packaging. The packaging would probably takes about 5 minutes in the whole process. So I am not expecting much difference if you specify only 1 target to build.

To targeting just one single OS you have to specify the target environment in the parent pom.xml file (see Tycho - Target runtime environment):
<plugin>
<groupId>org.eclipse.tycho</groupId>
<artifactId>target-platform-configuration</artifactId>
<version>${tycho-version}</version>
<configuration>
<environments>
<environment>
<os>win32</os>
<ws>win32</ws>
<arch>x86</arch>
</environment>
<environments>
</configuration>
</plugin>
If you use PDE Build instead of Maven/Tycho the Ant property is configs, e.g, -Dconfigs="win32, win32, x86".
FYI: Eclipse Platform CI which generates the Eclipse SDK archives

From https://wiki.eclipse.org/Platform-releng/Platform_Build#Building_natives
Optionally, you can pass -Dnative= parameter with one of the following options to compile the natives for the specified native.
cocoa.macosx.x86
cocoa.macosx.x86_64
gtk.linux.x86
gtk.linux.x86_64
win32.win32.x86
win32.win32.x86_64
win32.wce_ppc.arm
The arg would be -Dnative=win32.win32.x86_64

maven builds fails inside ubuntu vagrant machine as well as docker instance

I am developing an api using jaxb. The maven build (using jdk-7) works on my local windows machine. Now if I try to build it on my vagrant box (ubuntu/trusty64) after setting up maven and openjdk7 on the vm, I get following error on performing mvn clean install:
java.io.FileNotFoundException (operation not permitted)
There are in all 5 projects as part of my pom.xml, the first 3 (business and projects) gets built successfully, only the 4th one (which generates the war) file fails with this error when it is trying to generate the war file. Maven was successful in copying other files into the target folder for other projects.
Also, I am able to do perform maven builds on the same machine without errors on simple java projects (from https://maven.apache.org/guides/getting-started/maven-in-five-minutes.html)
My guess is the Vagrant Virtualbox VM is not is not able to allocate required resources to JVM but i am clueless on how i could do it. I did try to increase the memory footprint by setting the maven properties on my vm
export MAVEN_OPTS="-Xms1024m -Xmx4096m -XX:PermSize=1024m"
Detailed error:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.4:war (default-war) on project '<app>' : Could not copy webapp classes [/usr/src/<app>/target/classes]: /usr/src/<app>/target/<app>-03.00.00.01-SNAPSHOT/WEB-INF/classes/<my-app-src>/rest/config/ResourceConfig.class (Operation not permitted) -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.4:war (default-war) on project <my-app>: Could not copy webapp classes [/vagrant_data/<my-app-src>/<my-app>/target/classes]
[/vagrant_data/<my-app-src>/<my-app>/target/classes]
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:217)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:622)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Could not copy webapp classes [/vagrant_data/<my-apps-src>/target/classes]
at org.apache.maven.plugin.war.packaging.ClassesPackagingTask.performPackaging(ClassesPackagingTask.java:80)
at org.apache.maven.plugin.war.packaging.WarProjectPackagingTask.handleClassesDirectory(WarProjectPackagingTask.java:207)
at org.apache.maven.plugin.war.packaging.WarProjectPackagingTask.performPackaging(WarProjectPackagingTask.java:104)
at org.apache.maven.plugin.war.AbstractWarMojo.buildWebapp(AbstractWarMojo.java:505)
at org.apache.maven.plugin.war.AbstractWarMojo.buildExplodedWebapp(AbstractWarMojo.java:433)
at org.apache.maven.plugin.war.WarMojo.performPackaging(WarMojo.java:213)
at org.apache.maven.plugin.war.WarMojo.execute(WarMojo.java:175)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
... 19 more
Caused by: java.io.FileNotFoundException: /vagrant_data/<my-apps-src>/target/<my-app>-03.00.00.01-SNAPSHOT/WEB-INF/classes/<my-app-src>/rest/config/ResourceConfig.class (Operation not permitted)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
at java.io.FileOutputStream.<init>(FileOutputStream.java:160)
at org.codehaus.plexus.util.FileUtils.doCopyFile(FileUtils.java:1068)
at org.codehaus.plexus.util.FileUtils.copyFile(FileUtils.java:1049)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask.copyFile(AbstractWarPackagingTask.java:334)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask$1.registered(AbstractWarPackagingTask.java:154)
at org.apache.maven.plugin.war.util.WebappStructure.registerFile(WebappStructure.java:207)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask.copyFile(AbstractWarPackagingTask.java:149)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask.copyFiles(AbstractWarPackagingTask.java:104)
at org.apache.maven.plugin.war.packaging.ClassesPackagingTask.performPackaging(ClassesPackagingTask.java:75)
... 27 more

it seems that you don't have permision to write in that folder.
you could try using chmod 777 . -R in the vagrant shared folder. Also before doing this you could check if you can create a new file in the target directory by "touch target/newFile".

Resolve workspace artifacts option in Eclipse generates error when one of the resolving projects is opened

I have a maven project A, with 4 submodules. I have another maven project B, without any submodules. One of the 4 submodules of A, references project B.
When I do clean install on project A, I receive an error message:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.2:war (default-war) on project dca-web: Failed to copy file for artifact [be.vlaanderen.dwse:dwse-doc-tools:jar:3.2.2:compile]: /Users/Fabrizio/ontwikkeling/projecten/doc-tools/target/classes (Is a directory)
When enabling debug information: it is clear what is the issue:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.2:war (default-war) on project dca-web: Failed to copy file for artifact [be.vlaanderen.dwse:dwse-doc-tools:jar:3.2.2:compile]: /Users/Fabrizio/ontwikkeling/projecten/doc-tools/target/classes (Is a directory) -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-war-plugin:2.2:war (default-war) on project dca-web: Failed to copy file for artifact [be.vlaanderen.dwse:dwse-doc-tools:jar:3.2.2:compile]
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:216)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:120)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:355)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:155)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:584)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:216)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:160)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoExecutionException: Failed to copy file for artifact [be.vlaanderen.dwse:dwse-doc-tools:jar:3.2.2:compile]
at org.apache.maven.plugin.war.packaging.ArtifactsPackagingTask.performPackaging(ArtifactsPackagingTask.java:131)
at org.apache.maven.plugin.war.packaging.WarProjectPackagingTask.handleArtifacts(WarProjectPackagingTask.java:190)
at org.apache.maven.plugin.war.packaging.WarProjectPackagingTask.performPackaging(WarProjectPackagingTask.java:109)
at org.apache.maven.plugin.war.AbstractWarMojo.buildWebapp(AbstractWarMojo.java:472)
at org.apache.maven.plugin.war.AbstractWarMojo.buildExplodedWebapp(AbstractWarMojo.java:404)
at org.apache.maven.plugin.war.WarMojo.performPackaging(WarMojo.java:215)
at org.apache.maven.plugin.war.WarMojo.execute(WarMojo.java:177)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:132)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
... 19 more
Caused by: java.io.FileNotFoundException: /Users/Fabrizio/ontwikkeling/projecten/doc-tools/target/classes (Is a directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:138)
at org.codehaus.plexus.util.io.FileInputStreamFacade.getInputStream(FileInputStreamFacade.java:36)
at org.codehaus.plexus.util.FileUtils.copyStreamToFile(FileUtils.java:1141)
at org.codehaus.plexus.util.FileUtils.copyFile(FileUtils.java:1048)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask.copyFile(AbstractWarPackagingTask.java:293)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask$1.registered(AbstractWarPackagingTask.java:150)
at org.apache.maven.plugin.war.util.WebappStructure.registerFile(WebappStructure.java:211)
at org.apache.maven.plugin.war.packaging.AbstractWarPackagingTask.copyFile(AbstractWarPackagingTask.java:145)
at org.apache.maven.plugin.war.packaging.ArtifactsPackagingTask.performPackaging(ArtifactsPackagingTask.java:106)
But the folder target/classes is a directory! So there is a bug somewhere in one of the maven plugins I guess...
When I close project B, there is no problem. So opening the referenced project creates an issue...
I need to have project B open, because I use project A as a web application in Tomcat. When I have project B open and i change a file and save it, Eclipse does an incremental publish, and therefore Tomcat doesn't need to redeploy or restart! This saves me for each file change like 30 seconds! So it is very important to keep this project open...

I found the solution. Apparently eclipse luna (or any eclipse luna based ide) is using an embedded version of maven, which in turn uses the maven-war-plugin version 2.2. After adding in my pom the version 2.6, it solved the issue!
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.6</version>
</plugin>
</plugins>
</build>

Occasional error when building an eclipse feature with a Tycho project

I have a Maven/Tycho build of an OSGi based application that occasionally fails with an exception.
I have about 20 eclipse features, and it doesn't seem to have anything to do with the actual feature (it can be a different feature that fails every time, and often the build works fine)
It's no disaster, but I'd like the fix this at some point, and I don't really know how to debug this further short of diving into Tycho code or starting to mess with random settings.
Does this ring a bell with anyone?
System: Fedora Linux
JVM: OpenJDK Runtime Environment (IcedTea6 1.11.3) (fedora-67.1.11.3.fc16-x86_64)
Maven: 3.0.3
Tycho: 0.15.0
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.eclipse.tycho:tycho-packaging-plugin:0.15.0:package-feature (default-package-feature) on project com.dexels.navajo.tipi.swing.feature: Execution default-package-feature of goal org.eclipse.tycho:tycho-packaging-plugin:0.15.0:package-feature failed: com.dexels.navajo:com.dexels.navajo.tipi.swing.deps:eclipse-plugin:1.2.1-SNAPSHOT does not provide an artifact with classifier 'null'
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:225)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:319)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239)
at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:98)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:64)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:287)
at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:679)
Caused by: org.apache.maven.plugin.PluginExecutionException: Execution default-package-feature of goal org.eclipse.tycho:tycho-packaging-plugin:0.15.0:package-feature failed: com.dexels.navajo:com.dexels.navajo.tipi.swing.deps:eclipse-plugin:1.2.1-SNAPSHOT does not provide an artifact with classifier 'null'
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:110)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
... 27 more
Caused by: java.lang.IllegalStateException: com.dexels.navajo:com.dexels.navajo.tipi.swing.deps:eclipse-plugin:1.2.1-SNAPSHOT does not provide an artifact with classifier 'null'
at org.eclipse.tycho.packaging.FeatureXmlTransformer$1.visitPlugin(FeatureXmlTransformer.java:62)
at org.eclipse.tycho.core.osgitools.AbstractArtifactDependencyWalker.traversePlugin(AbstractArtifactDependencyWalker.java:215)
at org.eclipse.tycho.core.osgitools.AbstractArtifactDependencyWalker.traverseFeature(AbstractArtifactDependencyWalker.java:86)
at org.eclipse.tycho.core.osgitools.AbstractArtifactDependencyWalker.traverseFeature(AbstractArtifactDependencyWalker.java:63)
at org.eclipse.tycho.packaging.FeatureXmlTransformer.transform(FeatureXmlTransformer.java:47)
at org.eclipse.tycho.packaging.PackageFeatureMojo.expandVersionQualifiers(PackageFeatureMojo.java:300)
at org.eclipse.tycho.packaging.PackageFeatureMojo.execute(PackageFeatureMojo.java:120)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
... 28 more

This could be related to
the availability of the item in the local Maven repository and/or remote Maven repositories
the build phase you are executing.
If the included eclipse-plugin has a version that is not in any Maven repositories, and you only execute the build up to a lifecycle phase which does not include install, you may be able to reproduce the problem.
If you manage to pin down the problem, this would make a good bug report for Tycho.