Installing and using HDF5 for Eclipse on Mac OSx - java

I am trying to install and use the HDF5 libraires in eclipse in order to read and manipulate a dataset for my Big Data class.
I followed the instructions from the following website : http://www.hdfgroup.org/products/java/release/downloadsrc.html
At the end of the installation, after the command
ctest -S HDFJAVAMacCMake.cmake -C Release -V -O hdf-java.log
I get the following message :
100% tests passed, 0 tests failed out of 313
Total Test time (real) = 39.85 sec
[ERROR_MESSAGE]
Error in read script: /Users/fg/Downloads/build/HDFJAVAMacCMake.cmake
I don't understand why I get the Error in read script after every test passed.
Was the installation successful or not ? If yes, how do I manage to link the hdf5 libraries into my eclipse project ?
Thanks a lot for your time!

Okay, I managed to link and use the library in Eclipse. For those with the same problem, here is what I did.
After building the HDF-java software with cmake (as described in the link I provided), I still get the error message
[ERROR_MESSAGE]
Error in read script: /Users/fg/Downloads/build/HDFJAVAMacCMake.cmake
But everything has been compiled successfully (I still don't know why I get this message though).
Then, the following dmg appears in the build directory HDFView-2.10.1-Darwin.dmg (for version 2.10.1 of course). You need open it and drag it to your application folder. This "app" (right click, Show Package Content) contains the java libraries for HDF4 and HDF5, as well as the native librairies (.dylib for mac osx).
The paths are the following,
JARs files : /Applications/HDFView.app/Contents/Java
Native libs: /Applications/HDFView.app/Contents/Resources/lib
At this point, you can open Eclipse and go to the "Build Path Configuration" of your project and provide both the JARs and the native lib path.
Under the Libraries tab, you have to provide all the JARs contained in the first path I mentioned above. Then, go to the Source tab and you should see Native library location under your project. Simply give the second path I mentioned above.
Now you should be able to use the HDF libraries and compile your project without exception.
Hope this helps!

Related

Minecraft forge 1.14.4: missing library error (snapshot) in eclipse

I am trying to start modding Minecraft using Forge 1.14.4 but because of a "missing library" which is a snapshot, I will not be able to.
I have tried relentless online research but it never comes up.
In build.gradle, I noticed a part saying:
mappings channel: 'snapshot', version: '20190719-1.14.3'
The files being missing is preventing the project from being built.
The problem can be caused by having the wrong version of Java on your system path.
First, make sure you have the right JDK installed - jdk1.8.0_202 currently works for me. Download and install it if you haven't already.
Next, make sure it's the first version of Java in your path.
In Windows 10, press start, type 'Edit the system environment variables", and click Environment Variables.
Look for Path in the the System variables (the lower half of the screen, not the top half which may also have a Path variable).
There may be multiple lines that reference Java. On my computer I had two: C:\ProgramData\Oracle\Java\javapath and C:\Program Files\Java\jdk1.8.0_202\bin. I deleted the first reference.
Open a new console and run the gradlew commands from README.txt again
Some library is missing. Run the command gradlew eclipse after navigating into your project directory.
Is vecmath inside your build paths? I often had problems with it, but you can implement it manually.

Ant Automation of Netbeans

I am trying to automate the build of a project, right now if I build using Ant it fails.
If I build with netbeans it is successful. (though sometimes I have to restart netbeans if I've made any changes like a svnrevert, or other things I've tried)
If I build with ant after the netbeans build it is successful.
Any pointers on how to troubleshoot this?
I've searched high and low for how to deal with this but have no idea. the build.xml and other build related files are autogenerated from netbeans as far as I can tell.
This is the error I am getting when I try building straight with Ant
C:\Users\...\nbproject\xml_binding_build.xml:6: typedef class com.sun.tools.xjc.XJCTask can
t be found
using the classloader AntClassLoader[]
EDIT:
The result with debug enabled doesn't really give any additional info besides a stack trace
"Netbeans projects uses nbproject/private directory to contain some system dependent attributes.Netbeans puts the JAXB path information in this directory, which cause my the compilation problem.
jaxws.endorsed.dir=D:\Program Files\NetBeans 6.7.1\java2\modules\ext\jaxws21\api:D:\Program Files\NetBeans 6.7.1\ide11\modules\ext\jaxb\api
This could be a bug of JAXB Wizard in Netbeans.
Solution:
Create another project in the current Netbeans environment and run JAXB Wizard once. Look at the nbproject/private/private.properties file, copy the corresponding line into your target JAXB application, clean and build the application."
Source: http://braveo.blogspot.ca/2009/11/netbeans-jaxb-problem-typedef-class.html
In my case, it looked like the private.properties (and private.xml) files were never checked in, so unless they had been built at least once by netbeans my build would continue to fail. I checked those files in and the build is successful now.

Android : source not found [duplicate]

While debugging a java app in eclipse I receive a "Source not found" error in two cases:
Stepping in to a file in a different project which is already imported
Stepping in to a file in an installed maven repository
The files are there, but eclipse won't step into them, instead it shows a button to "attach source"
I tried attaching (which opened a dialog to define a variable?!) and eclipse did jump to the file, but the debugger could not inspect any variables there. Also manually attaching the source for each dependency isn't practical, as in my case there are thousands of dependency files.
Why is this happening, and how can it be resolved?
Just 3 steps to configuration Eclipse IDE:
Note: After updating the Source Lookup paths, you'll have to stop and restart your debug session. Otherwise, the file with the missing source will continue to show "missing source".
Edit Source Lookup
Select the Edit Source Lookup... command [ Edit Source Lookup ] to open the Source Path Dialog, which allows you to make changes to the source lookup path of the selected debug target.
IMPORTANT Restart Eclipse after this last step.
Eclipse debugging works with the class actually loaded by the program.
The symptoms you describe sounds like the class in question was not found in the project, but in a distribution jar without debug info found before the project you are working with.
This can happen for several reasons but have a look at the location where the classes showing this behaviour is found (look in the navigation pane to identify it). You will most likely need to change the build path of the project to avoid using this jar and have the JVM use the project instead.
EDIT: Note that as of 2018 it is common to use a build framework like Maven, where the build path is managed by the m2e plugin so this problem should be very less frequent than when the question was asked. If you use Maven and m2e, make sure to enable Preferences / Maven / "Download Artifact Sources" or right-click the project, Maven / "Download Sources".
The symptoms perfectly describes the case when the found class doesn't have associated (or assigned) source.
You can associate the sources for JDK classes in Preferences > Java > Installed JRE. If JRE (not JDK) is detected as default JRE to be used, then your JDK classes won't have attached sources. Note that, not all of the JDK classes have provided sources, some of them are distributed in binary form only.
Classes from project's build path, added manually requires that you manually attach the associated source. The source can reside in a zip or jar file, in the workspace or in the filesystem. Eclipse will scan the zip, so your sources doesn't have to be in the root of the archive file, for example.
Classes, from dependencies coming from another plugins (maven, PDE, etc.). In this case, it is up to the plugin how the source will be provided.
PDE will require that each plugin have corresponding XXX.source bundle, which contains the source of the plugin. More information can be found here and here.
m2eclipse can fetch sources and javadocs for Maven dependencies if they are available. This feature should be enabled m2eclipse preferences (the option was named something like "Download source and javadocs".
For other plugins, you'll need to consult their documentation
Classes, which are loaded from your project are automatically matched with the sources from the project.
But what if Eclipse still suggest that you attach source, even if I correctly set my classes and their sources:
This almost always means that Eclipse is finding the class from different place than you expect. Inspect your source lookup path to see where it might get the wrong class. Update the path accordingly to your findings.
Eclipse doesn't find anything at all, when breakpoint is hit:
This happens, when you are source lookup path doesn't contain the class, which is currently loaded in the runtime. Even if the class is in the workspace, it can be invisible to the launch configuration, because Eclipse follows the source lookup path strictly and attaches only the dependencies of the project, which is currently debugged.
An exception is the debugging bundles in PDE. In this case, because the runtime is composed from multiple projects, which doesn't have to declare dependencies on one another, Eclipse will automatically find the class in the workspace, even if it is not available in the source lookup path.
I cannot see the variables when I hit a breakpoint or it just opens the source, but doesn't select the breakpoint line:
This means that in the runtime, either the JVM or the classes themselves doesn't have the necessary debug information. Each time classes are compiled, debug information can be attached. To reduce the storage space of the classes, sometimes this information is omitted, which makes debugging such code a pain. Your only chance is to try and recompile with debug enabled.
Eclipse source viewer shows different lines than those that are actually executed:
It sometimes can show that empty space is executed as well. This means that your sources doesn't match your runtime version of the classes. Even if you think that this is not possible, it is, so make sure you setup the correct sources. Or your runtime match your latest changes, depending on what are you trying to do.
From http://www.coderanch.com/t/587493/vc/Debugging-Eclipse-Source
"When running in debug mode, right click on the running thread (in threads tab) and select Edit Source Lookup. At this point, you should be able to add the necessary project/jar which contains your source code."
I added my current project in this way, and it solved my problem
I had similar problem with my eclipse maven project. I fought with this issue quite a long time then I tried to rebuild project with
mvn clean eclipse:eclipse
and it helped.
Note: Using this approach will confuse the m2e plugin since the two approaches are very different. m2e adds a virtual node to your project called "Maven Dependencies" and asks Maven to add all dependencies there.
mvn eclipse:eclipse, on the other hand, will create a lot of individual entries in the file .classpath. Eclipse will handle them as if you manually added JARs to your project.
Unless you know how the classpath in Eclipse works, this approach is not recommended.
I was facing the same issue,I followed the bellow steps.
Window => Preferences => Java => Installed JREs,
You see in the above screen Jre1.8.0_12 is selected.
select the JRE you are using and click Edit. Now You should see the bellow screen.
Click on the directory, browse for Jdk, It should look like bellow screen.
click ok, and its done
I had the problem that my Eclipse was not debugging the source code of my project. I was getting a blank page with "Source code node found".
Please click the Attach source code button. Then delete the "default" folder then click add and go to your project location and attach. This worked for me
Remove the existing Debug Configuration and create a new one. That should resolve the problem.
None of the mentioned answer worked for me.
To resolve this issue i have to follow bellow steps:
Right click on Java HotSpot(TM) 64 Bit server.
Select "Edit Source Lookup".
Click on "Add".
Select "File System Directory" instead of Java project.
Select Root directory of your project.
Check "Search Subfolders".
Click Ok ok ok.
Thanks.
Click -> Edit Source Lookup Path
after then
Click -> Add finally select Java project and select project path.
Source: https://www.youtube.com/watch?v=IGIKPY6q1Qw
In my case, even after Editing source lookup and Adding project, it didn't worked. I configured the Build path of the project.
After that, I selected JRE System Library and it worked.
Evidently, Eclipse does not automatically know where the source code for the dependent jars are. It is not clear why debugger could not inspect variables once the source was attached. One possibility is incorrect/incompatible source.
Assuming you have a maven project and the sources of the dependencies are downloaded and available in the local repository, you may want to install m2eclipse, the maven eclipse plugin and see if that helps in addressing your issue.
You might have source code of a dependency accessible to Eclipse. But Eclipse does not know for source code for code that is dynamically loaded. E.g. through Maven.
In case of Maven, I recommend that you use run-jetty-run plugin:
http://code.google.com/p/run-jetty-run/
As a workaround you can also connect to a running JVM with the debugger and you will see the code.
Alternatively you can use Dynamic Source Lookup plugin for Eclipse from here:
https://github.com/ifedorenko/com.ifedorenko.m2e.sourcelookup
Unfortunately it didn't helped me as it has issues with Windows paths with spaces.
I have filled an enhancement request on Eclipse Bugzilla and if you agree this issue "Source not found" should vanish forever, please vote for it here:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=384065
Thanks!
Sasa
In my case in "Attach Source", I added the other maven project directory in the "Source Attachment Configuration" panel. Adding the latest version jar from the m2 repository din't work. All the classes from the other maven project failed to open.
Here test was my other maven project containing all the java sources.
I had the very same problem. In my case, I've disabled Window-Preferences-Java-Debug [Suspend execution on uncaught exceptions]. Then, the console showed me the correct error: my MySql user hadn't privileges to access the database. According to this topic.
Info: This is a possible solution, when you use maven (pom.xml) with couple of projects.
If you are working with maven, make sure what version you are taking inside the according pom.xml (e. g. 1.0.1-SNAPSHOT ).
It might be possible that your code is up-to-date, but your pom.xml dependencies are still taking the old JAR's/Snapshots (with the old code).
Finding the problem:
Try to debug the according file.
Therefore, set a breakpoint in the relevant code area.
When "source not found" appears, make sure to bind in the right project (where the .java file can be found).
The compile .class file opens up in the IDE editor.
Click "Link with Editor" to find the according JAR/Snapshot.
Now make sure that this JAR is the most recent one. Possibly there is a newer one. In that case, write the most recent version number in the pom.xml.
Then do a maven update and build (e. g. "mvn clean install -U") in the right project directory.
If you are on eclipse or STS please install and Use GC(GrepCode Plugin) ,some time you don't need to attach the source .zip file into your project path so GrepCode works fine for you.
I've had a related issue in connection with Glassfish server debugging in Eclipse.
This was brought about by loading the source code from a different repository (changing from SVN to GitHub). In the process, the wrong compiled classes were used by the Glassfish server and hence, the source and run time would be out of sync with break points appearing on empty lines.
To solve this, rename or delete the top folder of the classes directory and Glassfish will recreate the whole class directory tree including updating the class files with the correctly compiled version.
The classes directory is located in: /workspace/glassfish3122eclipsedefaultdomain/eclipseApps/< your Web Application>/WEB-INF/classes
In my case with tomcat projects I have checked project here:
Window - Preferences - Tomcat - Source Path - Add java projects to source path
In my case the Maven version of the other referenced project didn't match the version of the test project. Once they were the same, the problem disappeared.
When running in debug mode, click Edit Source Lookup after suspended from thread. At this point, we should be able to add the necessary project/jar which contains your source code.
After I added my current project in this way, and it solved my problem. Thanks
If you want to attach source code to any JAR by auto-downloading, try using this Eclipse plugin Java Source Attacher
I had this problem while working on java code to do process on a excel file containing a data set, then convert it to .csv file, i tried answers to this post, but they did not work.
the problem was the jar files themselves. after downloading needed jar files one by one(older releases) and add them to my project, "source not found" error vanished.
maybe you can check your jar files.
hope this would help.
this worked for me
right click on project -> Properties -> Deployment Assembly -> add your jar
Go to Debug configuration in eclipse and use below goal to run your application.
-Dmaven.surefire.debug
e.g
-Dmaven.surefire.debug exec:java
Well, here's what worked for me. I tried every possible solution on StackOverflow that there was. I tried changing my source location in the debug menu, I installed the m2e Eclipse plugin, I changed from embedded Maven, and I installed the run-jetty-run and nothing worked. Now, I will caveat that I was not trying to view an external person's source code, I just wanted to see my OWN code, but every time I "stepped in" to my methods that I wrote that were in MY project, I got the "Source now found" error.
After finally asking an expert, my issue was that the first thing Eclipse was doing was calling a ClassLoader, which you can see from the debug stack. All I had to do was F6 (step over) and then it took me back to my original call and then F5 (step in). And there was my code. Sigh...such a simple fix but an hour wasted.
For beginners,
There is a possibility that the jar file is a part of the project which you have not yet included in the Eclipse workspace.
For that, you need to know the project name of the jar file.
Say for example, its abc-18.0.0-SNAPSHOT.jar, it means that the project you are supposed to include in your workspace is abc.
I had the same issue with eclipse 2019-03 (4.11.0) and I was only able to solve this by doing the debugging via remote debugging instead of directly launching it in debug mode.
Attach source -> Add -> External Archive -> select the jar -> open -> done
the catch is look for the sources jar and attach this jar.
for example the jar ends with "-sources" Stax2-api-3.4.1-sources
sometimes these thing happens because of the version also like if you are using latest
version in that case it may arise try to use older version it will work.

Eclipse plugin not working properly

I developed an Eclipse plugin that compiles and runs java code in German. The technique I am using is that I translate the code to English and pass it to Java Compiler and get the results back and print it in the console.
The problem is that the plugin works when I run the plugin from Inside Eclipse but when I install the plugin in Eclipse so that when I open Eclipse it already exists there and start to test if a real user uses my plugin and creates a new Java project and try to the compile button in my plugin it says [The chosen operation is not currently available] ![Here is the the way I run and it opens a new Eclipse application with the installed plugin ]
Any help please
the way you installed your plugin sounds a little weird to me. So at first please try to export your plugin via the Export Wizard.
(Select Export -> Deployable plugins and features from your projects context menu)
Export your project as jar file and copy it to the 'plugin' folder of your eclipse instance.
After that it might be helpful to debug your plugin on OSGI-Level as there might be a problem loading your plugin (at least the error description you have posted indicates that).
Run eclipse with -console -noExit -consoleLog flags to open an OSGI console for debugging. After that try running ss <your-plugin-name> to see what the state of your plugin is.
The output gives you the ID of your plugin and the state it currently has. If the state of your plugin is not ACTIVE try running start <your-plugin-id> to see whether it starts correctly. If there is a problem starting your plugin you should get a respective log message. Feel free to post it here in case you need further help.
Otherwise there are plenty of options what might cause your problems, so maybe its better to try the steps I have described above before getting into details.
If you want to run eclipse plug-in withput using Eclipse Application , then you need to make a Feature project.
Now if your algorithm has something to do with system Path , you must
check Unpack plug-in and you should read the resource accordingly.
Like PLatformUI.getWorkBC() etc..
No other eclipse plug-in (jar) should be inside plugins directory of eclipse of same name of your plug-in. Ensure for this.

Build Machine: error: package net.rim.device.api.ui does not exist

I am trying to get our build machine to consistently build our Blackberry project (build using the Eclipse plugin not the JDE) on check-in. We are using Jenkins to call the project and sometimes it works but only after I've fired up the project in eclipse on the far machine but then restarting causes the error to come back.
The first error I get is (the following errors are all in the same vein):
[javac] c:\<path_to_project>\src\path\to\package\class.java:6: error: package net.rim.device.api.ui does not exist
And every other reference to a net.rim.* object. Clearly it's because it's not linking to the target net_rim_api.jar file but I can't figure out what on earth is going wrong. I've tried poking at the build.xml file but I just get more errors and other versions of this error in other threads turn out to be not the same thing.
I have tried installing and using BB-Ant (roughly following this tutorial) but it has not provided me with the solution - I'm prepared to admit that I may have made a mistake in the implementation but I followed it as closely as I could with the current project that I have.
I would appreciate any help that you can give me.
EDIT
So I've now altered the project to use <rapc> instead of <javac> which appears to do the linking to the .jar for you but it's still frustrating that you can't simply use the auto generated build.xml. Is this a known (and due to lack of information available on the internet, accepted) issue with Eclipse?
I went down the BB Ant build script road a year or so ago, got a lot of help on this site, and tried to document my progress on this site. Hopefully the links I place will help you and others.
I have marked this as "community wiki" since it doesn't directly answer the question but I do think it is useful.
Basic algorithm
My answer on this page shows the algorithm for a working build script (BlackBerry: create COD from JAR source file in Ant script). Perhaps this is more complicated than you are looking for, but it does show the relationship I found between javac and rapc.
To summarise, I wanted to include my SDK into the final build, and the steps were:
javac the SDK to create CLASS files
preverify the CLASS files
jar the SDK
Copy the SDK JAR file into the project
javac the project - use the SDK JAR as the classpath
preverify the project CLASS files (again, use the SDK JAR in the
classpath)
jar the project - add the SDK JAR as a zipfileset
jarjar this project JAR to refactor package names as required
Finally, run rapc on this JAR - it will find no duplicate COD files
& should run fine.
Please read the other answers on that page, since they offer great advice that I used in my end result.
Extra Info & Including a JAR into final output
I'd recommend this page just for the extra links that I included in it - the exact question is unrelated (BlackBerry - Ant script to include JAR in project without external dependancies).
Again, the value is in the answers that the other guys provided.
Misc
Here are a couple of links to other BB build script issues that I had - you or someone may find them useful:
BlackBerry - Ant build script for more complex apps
BlackBerry - final step of build process
Finally this one speaks to a mistake in the documentation when compiling your own code into a library for import into a different project:
BlackBerry - use own JAR file in own project

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