"JAVA Parse Exception" error in Qualimap after MacOSX upgrade - java

I recently upgraded my MacOSX system to Catalina and several files were placed automatically into "Relocated items" folder on my Desktop. I recently tried to run the following code which had previously worked:
qualimap bamqc -bam Sample1_sorted.bam -c -outdir QualiMap/Sample1_sorted
and received the following error:
Java HotSpot(TM) 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0
Error: Unable to initialize main class org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain
Caused by: java.lang.NoClassDefFoundError: org/apache/commons/cli/ParseException
I have seen many other posts related to this error but am unsure how to even go about trying some of the suggested solutions. I do not work directly with some of the applications/files mentioned in these forums, such as JAVA, Maven, AppAssembler, and the pom.xml file (I could not even find that file). As a result, I wished to ask about this error from the perspective of a biologist using qualimap.
How can I fix this error (with little knowledge of the above applications/files)? I can certainly work with these applications/files, but I would probably need more detailed/basic/low-level advice on how to access and modify them. Thank you!

It seems what qualimap is a java application someone else wrote. I would raise a ticket with whomever wrote this app.

Related

Oracle 11gR2 Design Center Can't find Java Virtual Machine

I'm having an issue with Oracle 11g R2 Design Center feature. When I click it, it gives me the error below:
C:\app[username]\product\11.2.0\dbhome_1\owb\bin\win32>call setowbenv.bat
WARNING: Unknown directive: SetSkipJ2SDKCheck
WARNING: Could not find jvm.cfg! in 'C:\app[username]\product\11.2.0\dbhome_1\jdk\jre\lib\jvm.cfg'
WARNING: Cannot find default VM "client" at C:\app[username]\product\11.2.0\dbhome_1\jdk
ERROR: Cannot find VM at: C:\app[username]\product\11.2.0\dbhome_1\jdk
Aborting!
I've tried many things to resolve this, as listed below:
Download 32b version of JDK (actually, I've downloaded multiple to rule out the version issue, both 32 and 64)
Point environment variable and path to JDK installation
Change sqldeveloper.cfg file to include SetJavaHome {path to JDK}
Move the jvm.cfg file to the directory it's expected to be at
Checked the paths to ensure the expected files were there
With step 4, after doing so I receive a different error message:
"Client VM is unsupported"
With step 5, after doing so I realized the path to the executable was not in:
C:\app[username]\product\11.2.0\dbhome_1\jdk
But instead in:
C:\app[username]\product\11.2.0\dbhome_1\jdk\bin
So, from all of this I feel that if I can change the path the Oracle Design Center is using to the correct path, then this should resolve. Problem is, I'm unsure where to find this. Also, if it helps I believe the Design Center uses JDeveloper, since the error suggests to view the Oracle 9i JDeveloper Install Guide at jdev\install.html. I tried going to this link but I'm not sure if it exists anymore because it took me to Google. I chose the most relevant link but still, I did not find any information regarding this issue. If anyone can help I'd be very thankful, this has been running me in circles for 3 days now.
TIA

Unable to Connect to PowerDesigner through java

I have a requirement to automate the process of connecting to PowerDesigner through java to extract the models from repository. I have used the OLE Automation JavaProxy document to configure the process.
when trying to run, I'm getting this error:
Exception in thread "main" java.lang.NoSuchMethodError: org.eclipse.swt.internal.ole.win32.COM.CoCreateInstance(Lorg/eclipse/swt/internal/ole/win32/GUID;IILorg/eclipse/swt/internal/ole/win32/GUID;[I)I
at
com.sybase.stf.powerdesigner.PdCommon.Application.start(Application.java:57)
at
com.sybase.stf.powerdesigner.PdCommon.Application.(Application.java:31)
at
com.sybase.stf.powerdesigner.PdCommon.Application.getInstance(Application.java:42)
at OOM.src.createOOM.CreateOOM.CreateAndDisplayOOM(CreateOOM.java:37)
at OOM.src.createOOM.CreateOOM.main(CreateOOM.java:28)
Versions:
PowerDesigner - 16.5.5.0
Eclipse 4.18
Supporting Jars:
pdj2com_16.5.5.jar
org.eclipse.swt.win32.win32.x86_64_3.115.100.v20201202-1103.jar
The above issue is resolved Thanks!
Now i'm facing trouble connecting again with the below issue.
org.eclipse.swt.SWTException: Action can not be performed. result = -2137456383 (com.sybase.stf.powerdesigner.com.COMException: COM Failure [HRESULT: 0x80990101])
at org.eclipse.swt.ole.win32.OLE.error(OLE.java:345)
at com.sybase.stf.powerdesigner.com.COMException.raiseOnFail(COMException.java:83)
at com.sybase.stf.powerdesigner.com.IDispatchEx.raisingInvoke(IDispatchEx.java:231)
at com.sybase.stf.powerdesigner.PdCommon.IApplication.CreateModel(IApplication.java:84)
at OOM.src.createOOM.CreateOOM.createOOM(CreateOOM.java:68)
at OOM.src.createOOM.CreateOOM.CreateAndDisplayOOM(CreateOOM.java:42)
at OOM.src.createOOM.CreateOOM.main(CreateOOM.java:28)
Caused by: com.sybase.stf.powerdesigner.com.COMException: COM Failure [HRESULT: 0x80990101]
at com.sybase.stf.powerdesigner.com.COMException.raiseOnFail(COMException.java:88)
... 5 more
Is there anything else to add to the code to connect?
I am not able to find any solution online. Kindly help me figure this out. Thanks in advance.
The swt.win.win32.x86_64 jar is for 64-bit, so I assume you're using a 64-bit Java.
In my case, the pdj2com jar is named something like pdj2com_16.N.Nx64.jar for the 64-bit version. pdj2com_16.N.N.jar is the name of the 32-bit version.

Using eclipse with processing, cannot get java application to run

so i am just trying eclipse with processing and are having a problem with getting the java application to run.
I am basically following this tutorial: https://processing.org/tutorials/eclipse/
I have followed the steps but when i get to this part:
import processing.core.PApplet;
public class UsingProcessing extends PApplet{
public static void main(String[] args) {
PApplet.main("UsingProcessing");
}
}
No errors or nothing but when i press run (run as java application), a java program opens (no window, i can just see the program in the bottom part of the screen). Then it closes after a couple of seconds.
I also get the following errors:
java.lang.NoClassDefFoundError: com/apple/eawt/QuitHandler
at java.base/java.lang.Class.getDeclaredMethods0(Native Method)
at java.base/java.lang.Class.privateGetDeclaredMethods(Class.java:3119)
at java.base/java.lang.Class.getMethodsRecursive(Class.java:3260)
at java.base/java.lang.Class.getMethod0(Class.java:3246)
at java.base/java.lang.Class.getMethod(Class.java:2065)
at processing.core.PApplet.runSketch(PApplet.java:10707)
at processing.core.PApplet.main(PApplet.java:10504)
at processing.core.PApplet.main(PApplet.java:10486)
at UsingProcessing.main(UsingProcessing.java:6)
Caused by: java.lang.ClassNotFoundException: com.apple.eawt.QuitHandler
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)
... 9 more
That part of code should at least give me an empty sketch but i get nothing..
This guy got it to work but i cant.. https://www.youtube.com/watch?v=0cqSjyvA8EY
I can assure you that i have imported the processing library correct, so that is not where the problem lays. I believe that it is some problem with my java? I am using a macbook pro and the following java:
Java(TM) SE Runtime Environment 18.3 (build 10.0.1+10)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.1+10, mixed mode)
Thankful for all the help and I am kind of new to this so please be gentle if anything is wrong!
EDIT:
I have also tried with IntelliJ without luck, the same thing, java opens for a brief moment and then closes. This video was my guide: https://www.youtube.com/watch?v=_h2GZgnPcnM
I can assure you that i have imported the processing library correct, so that is not where the problem lays.
You need more than just the core.jar library. In your case you need whatever .jar file contains the com/apple/eawt/QuitHandler class.
This answer says that the .jar you're looking for comes with the Mac JDK. Try adding that .jar file to your classpath.
So i believe the problem is sort of solved. The problem was (i think) with the java that apple uses(?). So i downgraded to the Processing 2 core.jar and everything worked fine.
Found here: https://github.com/processing/processing/issues/5371
and a link that i did not fully understand : https://github.com/processing/processing/wiki/Supported-Platforms#java-9
The guy there suggests that you should downgrade your jdk(?), but I think that it was processing 2 that was discussed (when i did that it did not work). So for now, everything in eclipse done with processing has to be done with processing 2.
This is strange because the tutorial on processings website made it work with processing 3
EDIT: the previous answer was asked more than five years ago..

JBOSS came UP but GUI doesn't

Recently, we were facing some issues related to timesten configuration and as per Oracle's suggestion we gave a system reboot to verify the changes.
Post system reboot we found that one of our internal GUI ( related to the application ) didn't came up automatically. Although we restarted the JBOSS process manually post-reboot , process came UP well but GUI doesn't.
I went through the JBOSS startup.log as well but found to see so many errors there like:
error installing to real name=vfsfile jboss
org.jboss.deployers.spi.DeploymentException: Error deploying: jboss:service=Hypersonic,database=localDB
ERROR [AbstractKernelController] Error installing to Start: name=jboss:database=localDB,service=Hypersonic state=Create mode=Manual requiredState=Installed
log4j error: setFile(null,true) call failed.
java.sql.SQLException: The database is already in use by another process: org.hsqldb.persist.NIOLockFile
........and many more
Literally, i have gone through every possible workaround available on internet with no success. Please pardon my question's framing methodology if it's sounds too be least technical.
I am new to JBOSS so need your help in resolving this issue.
Environment is Solaris 10 and JBOSS version is "jboss-5.1.0.GA"

UnsatisfiedLinkError and NoClassDefFoundError : Running Java Mapscript on Ubuntu 11.10

We have coded and run a dynamic web application using MAPSERVER(Version 6.0.1) on windows platform using Java Technology. Now, there is need of deploying it on Ubuntu 11.10. We have installed Apache Tomcat 6.0, Mapserver 6.0.1, Apache 2.0, and FWTools-2.0.1(As this package contain all required tools for mapserver if I am not wrong, so I didn't feel any other tools to be installed). We have deployed the war file(and put application without) in Apache Tomcat 's Webapps folder. I even got the index page which dont have code related with mapscript api. But while fetching the other servlet with mapscript we are getting following error...
java.lang.UnsatisfiedLinkError: no mapscript in java.library.path
java.lang.ClassLoader.loadLibrary(ClassLoader.java:1681)
java.lang.Runtime.loadLibrary0(Runtime.java:840)
java.lang.System.loadLibrary(System.java:1047)
edu.umn.gis.mapscript.mapscriptJNI.<clinit>(mapscriptJNI.java:23)
edu.umn.gis.mapscript.mapObj.<init>(mapObj.java:283)
Again while refreshing the browser page where the above error was displayed, I got a change,
java.lang.NoClassDefFoundError: Could not initialize class
edu.umn.gis.mapscript.mapscriptJNI
edu.umn.gis.mapscript.mapObj.<init>(mapObj.java:283)
I searched on net about the above problem. But finally blank. Please, provide idea about the above problem.
I'm not going to explain why you're getting the UnsatisfiedLinkError, but instead I'll explain why you are getting the NoClassDefFoundError when you reload the page.
A NoClassDefFoundError with a message Could not initialize class ... is thrown by the JVM when it attempts to initialize a class that it has already tried and failed to initialize.
The first of your two stacktraces contains the line
edu.umn.gis.mapscript.mapscriptJNI.<clinit>(mapscriptJNI.java:23)
The method name <clinit> denotes the static initializer, of the class mapscriptJNI. So, at the point that the UnsatisfiedLinkError was thrown, the JVM was trying to initialize this class. Looking at the error message, it seems that this static initializer tried to load the native code library mapscript but failed.
This UnsatisfiedLinkError causes the mapscriptJNI class to fail to initialize successfully. The JVM keeps a record of all classes that fail to initialize, and if you attempt to initialize one of those classes again, you'll get a NoClassDefFoundError with a message saying that it could not initialize that class.
When you refresh the page, you end up causing the JVM to attempt to initialize the class mapscriptJNI a second time. Of course, this class failed to initialize the previous time. Your second stacktrace contains exactly the error I've described.
In short, the UnsatisfiedLinkError is the real error here. Fix that and the other one will go away.
I would check the following 2 items:
Is the mapscript.jar file on Tomcat or at least your webapp's classpath? (NoClassDefFoundError is your big clue here)
Is the libmapscript.so on either your LD_LIBRARY_PATH or -Djava.library.path? (UnsatisfiedLinkError since the shared object cannot be found)
Try having a look at this post, near the Running Java Mapscript (on Linux) section.
Hope that helps!

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