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Log4j removal issue

I'm trying to remove Log4j from my project. The project is building sucessfully after removing but I'm getting this error while running the build.
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/azuga]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:162)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:755)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:731)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:973)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1850)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.NoClassDefFoundError: Lorg/apache/log4j/Logger;
at java.base/java.lang.Class.getDeclaredFields0(Native Method)
at java.base/java.lang.Class.privateGetDeclaredFields(Class.java:3062)
at java.base/java.lang.Class.getDeclaredFields(Class.java:2249)
at org.apache.catalina.util.Introspection.getDeclaredFields(Introspection.java:106)
at org.apache.catalina.startup.WebAnnotationSet.loadFieldsAnnotation(WebAnnotationSet.java:269)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationFilterAnnotations(WebAnnotationSet.java:109)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationAnnotations(WebAnnotationSet.java:68)
at org.apache.catalina.startup.ContextConfig.applicationAnnotationsConfig(ContextConfig.java:336)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:776)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:307)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:95)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5262)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
... 10 more
Caused by: java.lang.ClassNotFoundException: org.apache.log4j.Logger
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1352)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1180)
... 24 more
I've tried removing dependencies I suspected to be using Log4j.

As a general advice, use a tool to manage your project's dependencies such as Gradle or Maven. These tools are capable of analyzing not only classpath dependencies but also runtime dependencies. That way, you can just see what the dependencies are - rather than suspecting.

Jacoco - method code too large when using ver 0.7.6 and 0.7.5

I am trying to set up to run Jacoco agent (http://mvnrepository.com/artifact/org.jacoco/org.jacoco.agent/0.7.6.201602180812), and I am getting an exception as below.
java.lang.instrument.IllegalClassFormatException: Error while instrumenting class ...
at org.jacoco.agent.rt.internal_14f7ee5.CoverageTransformer.transform(CoverageTransformer.java:93)
at sun.instrument.TransformerManager.transform(TransformerManager.java:188)
at sun.instrument.InstrumentationImpl.transform(InstrumentationImpl.java:428)
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:760)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(WebappClassLoaderBase.java:3114)
at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClassLoaderBase.java:1342)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1823)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1703)
at org.apache.catalina.util.Introspection.loadClass(Introspection.java:143)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationServletAnnotations(WebAnnotationSet.java:132)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationAnnotations(WebAnnotationSet.java:65)
at org.apache.catalina.startup.ContextConfig.applicationAnnotationsConfig(ContextConfig.java:415)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:892)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:386)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5405)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1574)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1564)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Error while instrumenting class org/apache/jsp/isml2jsp/cartridges/app_005fbusiness_005fmanager/default_/product/batch/AttributeValue_002d37d0cd03a157eeffaecd90c11598827569e0327d_jsp.
at org.jacoco.agent.rt.internal_14f7ee5.core.instr.Instrumenter.instrumentError(Instrumenter.java:152)
at org.jacoco.agent.rt.internal_14f7ee5.core.instr.Instrumenter.instrument(Instrumenter.java:103)
at org.jacoco.agent.rt.internal_14f7ee5.CoverageTransformer.transform(CoverageTransformer.java:91)
... 25 more
Caused by: java.lang.RuntimeException: Method code too large!
at org.jacoco.agent.rt.internal_14f7ee5.asm.MethodWriter.getSize(MethodWriter.java:2036)
at org.jacoco.agent.rt.internal_14f7ee5.asm.ClassWriter.toByteArray(ClassWriter.java:827)
at org.jacoco.agent.rt.internal_14f7ee5.core.instr.Instrumenter.instrument(Instrumenter.java:84)
at org.jacoco.agent.rt.internal_14f7ee5.core.instr.Instrumenter.instrument(Instrumenter.java:101)
... 26 more
The Java Option to run the Jacoco agent is set as:
JAVA_OPTS=$JAVA_OPTS\ -javaagent:/myserver/tomcat/lib/jacocoagent.jar=destfile=/tmp/jacoco.exec
I am not using a Maven or Ant file to run it, and the option to run the agent is set directly in the Tomcat startup script. Can anyone please help?

can't starting Tomcat v8.0 at localhost

I tried to create/run a java web app and ran into the following error. I saw that other people have had similar problems, however, I tried what they said but they all not work.
A child container failed during start
java.util.concurrent.ExecutionException: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/CourseServer]]
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:916)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:871)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1408)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1398)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/CourseServer]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:153)
... 6 more
Caused by: java.lang.NoClassDefFoundError: org/json/JSONException
at java.lang.Class.getDeclaredFields0(Native Method)
at java.lang.Class.privateGetDeclaredFields(Class.java:2583)
at java.lang.Class.getDeclaredFields(Class.java:1916)
at org.apache.catalina.util.Introspection.getDeclaredFields(Introspection.java:106)
at org.apache.catalina.startup.WebAnnotationSet.loadFieldsAnnotation(WebAnnotationSet.java:256)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationServletAnnotations(WebAnnotationSet.java:132)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationAnnotations(WebAnnotationSet.java:65)
at org.apache.catalina.startup.ContextConfig.applicationAnnotationsConfig(ContextConfig.java:334)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:783)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:305)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:95)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5154)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
... 6 more
Caused by: java.lang.ClassNotFoundException: org.json.JSONException
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1308)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1142)
... 20 more
and what's in my WEB-INF/lib
Help!

add below dependency into your pom.xml
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>20160212</version>
</dependency>
If you are not using maven then you have to download and add this java-json.jar to your build path

NoClassDefFoundError: org/json/JSONException means it can't find the class JSONException at runtime. Either you add it as a dependency in your pom.xml, add it to your build-path or you add the JAR to your Tomcat Lib folder.
Either way, you'll have to get the JAR containing the JSONException. Which can be found here.

I tried all the means,they all not work until I reinstall tomacat....

Dbutils error: java.sql.SQLException: net.sourceforge.jtds.jdbc.Driver

I'm implementing Dbutils using net.sourceforge.jtds.jdbc.Driver driver in jtds package.
Problem is it gives me java.sql.SQLException: net.sourceforge.jtds.jdbc.Driver error even after including jtds jar in project. It works fine when i include this jtds jar file in lib folder of tomcat.
I checked build code, jtds jar file is present there.
java.sql.SQLException: net.sourceforge.jtds.jdbc.Driver
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:254)
at org.apache.tomcat.jdbc.pool.PooledConnection.connect(PooledConnection.java:182)
at org.apache.tomcat.jdbc.pool.ConnectionPool.createConnection(ConnectionPool.java:702)
at org.apache.tomcat.jdbc.pool.ConnectionPool.borrowConnection(ConnectionPool.java:634)
at org.apache.tomcat.jdbc.pool.ConnectionPool.init(ConnectionPool.java:488)
at org.apache.tomcat.jdbc.pool.ConnectionPool.<init>(ConnectionPool.java:144)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.pCreatePool(DataSourceProxy.java:116)
at org.apache.tomcat.jdbc.pool.DataSourceProxy.createPool(DataSourceProxy.java:103)
at com.cibil.crs.escalationmatrix.dbutil.DataSourceFactory.createDataSource(DataSourceFactory.java:46)
at com.cibil.crs.escalationmatrix.dbutil.DataSourceFactory.createDataSource(DataSourceFactory.java:17)
at org.apache.tomcat.jdbc.pool.DataSourceFactory.getObjectInstance(DataSourceFactory.java:237)
at org.apache.naming.factory.ResourceFactory.getObjectInstance(ResourceFactory.java:143)
at javax.naming.spi.NamingManager.getObjectInstance(NamingManager.java:321)
at org.apache.naming.NamingContext.lookup(NamingContext.java:843)
at org.apache.naming.NamingContext.lookup(NamingContext.java:154)
at org.apache.naming.NamingContext.lookup(NamingContext.java:831)
at org.apache.naming.NamingContext.lookup(NamingContext.java:168)
at org.apache.catalina.core.NamingContextListener.addResource(NamingContextListener.java:1093)
at org.apache.catalina.core.NamingContextListener.createNamingContext(NamingContextListener.java:672)
at org.apache.catalina.core.NamingContextListener.lifecycleEvent(NamingContextListener.java:271)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5173)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:657)
at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1637)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.ClassNotFoundException: net.sourceforge.jtds.jdbc.Driver
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:270)
at org.apache.tomcat.jdbc.pool.PooledConnection.connectUsingDriver(PooledConnection.java:246)
Any idea?

You are using a connection pool and you are making use of the tomcat. See the link below, and notice the line that says "The fully qualified Java class name of the JDBC driver to be used. The driver has to be accessible from the same classloader as tomcat-jdbc.jar".
https://people.apache.org/~fhanik/jdbc-pool/jdbc-pool.html

Tomcat can't start the app because it can't find JSONRPC2ParseException class

I have application in /var/lib/tomcat7/webapps/code I have init.java file that use json-rpc-2.0
I compile it using:
export CLASSPATH=$CLASSPATH:/path/jsonrpc2-base-1.35.jar:/path/json-smart-1.2.jar
javac init.java
it compile but when I run the app (not the servlet) I got error 404 from Tomcat and in catalina.out file there is exception:
org.apache.catalina.LifecycleException: Failed to start component [StandardEngin
e[Catalina].StandardHost[localhost].StandardContext[/code]]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase
.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:87
7)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.jav
a:1114)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig
.java:1673)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:47
1)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
Caused by: java.lang.NoClassDefFoundError: com/thetransactioncompany/jsonrpc2/JSONRPC2ParseException
at java.lang.Class.getDeclaredFields0(Native Method)
at java.lang.Class.privateGetDeclaredFields(Class.java:2387)
at java.lang.Class.getDeclaredFields(Class.java:1796)
at org.apache.catalina.util.Introspection.getDeclaredFields(Introspection.java:106)
at org.apache.catalina.startup.WebAnnotationSet.loadFieldsAnnotation(WebAnnotationSet.java:261)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationServletAnnotations(WebAnnotationSet.java:140)
at org.apache.catalina.startup.WebAnnotationSet.loadApplicationAnnotations(WebAnnotationSet.java:67)
at org.apache.catalina.startup.ContextConfig.applicationAnnotationsConfig(ContextConfig.java:405)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:881)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:369)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5179)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
... 11 more
Caused by: java.lang.ClassNotFoundException: com.thetransactioncompany.jsonrpc2.JSONRPC2ParseException
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1714)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1559)
... 25 more
with caused by not found com/thetransactioncompany/jsonrpc2/JSONRPC2ParseException which is in jar file.
What's happening here? How can I fix it to make it work?

This is usually the jar files are not available for Tomcat.
The best way to solve this is place the json-rpc-2.0 jar files into your Tomcat's lib folder
Update
As specified by A4L user , you can also put the jar in your web applications WEB-INF/lib as well.