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Troubleshooting OpenMRS

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Created by user-5cf01, last modified by Glen McCallum on 2012-05-22

"Error Could not acquire change log lock" when installing or running database updates

When running each database changeset update, liquibase creates a row in the database table liquibasechangeloglock to prevent other applications/jars/users from trying to run updates at the same time. If Tomcat or OpenMRS crashes while an update is running, then the row will not be removed (unlocked). So the next time you start up you will see this error.

Solution

Clear out all rows in the libuibasechangeloglock table. With a command line SQL client, run the following command:
```
drop table liquibasechangeloglock;
```
If you normally use a GUI client for MySQL, find the liquibasechangeloglock table and drop it. Liquibase will recreate the table with the appropriate row during the next run.
Restart OpenMRS (e.g., restart Tomcat) and load the page again.

OpenMRS modules and settings disappear and reappear on reboot

A default Windows install of OpenMRS places its modules and properties files in "%APPDATA%\OpenMRS\". Where "APPDATA" is the home directory Application Data folder of the user that is running Tomcat.

Chances are your install is like most Windows installs, so the OpenMRS folder will be "C:\Documents and Settings\Your Username\Application Data\OpenMRS\". It is often the case that this account is in the Administrators group. Some Windows installs also have a default (but hidden) Administrator account (username: administrator, password: none) which under some circumstances can be used by Tomcat. In this case, the OpenMRS will be looking for its modules in the "C:\Application Data\OpenMRS\" folder. It will not find them there and thus modules and settings will not be loaded.

Solution

These problems stem from Windows services being run under the Local System account of the machine on which they are installed. Configure the Apache Tomcat service to start under a specific user account rather than the default "Local System Account". This can be configured in the Services window in Control Panel, Administrative Tools. You should use the same user account when running the installer.

Some module pages throw java.lang.ClassNotFoundException

There is an incompatibility between OpenMRS and versions of Tomcat later than 6.0.29, that means that modules which rely on custom EL functions will throw this exception. If encountering such an issue you should check which version of Tomcat you are using and if necessary downgrade to 6.0.29.

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1 Comment

user-4ba3b
Hi, This is the error i face while trying to compile the openmrs-core 1.9.x in ubunt, i have tried re-cloning the whole project and still the same error prevails. can you please help me?
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.openmrs.tools:openmrs-tools:jar:1.9.4-SNAPSHOT
[WARNING] 'build.pluginManagement.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-javadoc-plugin @ org.openmrs:openmrs:1.9.4-SNAPSHOT, /home/tika/fyp/git/openmrs-core/pom.xml, line 832, column 13
[WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ org.openmrs:openmrs:1.9.4-SNAPSHOT, /home/tika/fyp/git/openmrs-core/pom.xml, line 955, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.openmrs.test:openmrs-test:pom:1.9.4-SNAPSHOT
[WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ org.openmrs:openmrs:1.9.4-SNAPSHOT, /home/tika/fyp/git/openmrs-core/pom.xml, line 955, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.openmrs.api:openmrs-api:jar:1.9.4-SNAPSHOT
[WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ org.openmrs:openmrs:1.9.4-SNAPSHOT, /home/tika/fyp/git/openmrs-core/pom.xml, line 955, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.openmrs.web:openmrs-web:jar:1.9.4-SNAPSHOT
[WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ org.openmrs:openmrs:1.9.4-SNAPSHOT, /home/tika/fyp/git/openmrs-core/pom.xml, line 955, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.openmrs.web:openmrs-webapp:war:1.9.4-SNAPSHOT
[WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ org.openmrs:openmrs:1.9.4-SNAPSHOT, /home/tika/fyp/git/openmrs-core/pom.xml, line 955, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.openmrs:openmrs:pom:1.9.4-SNAPSHOT
[WARNING] 'build.pluginManagement.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-javadoc-plugin @ line 832, column 13
[WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ line 955, column 12
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] OpenMRS
[INFO] openmrs-tools
[INFO] openmrs-test
[INFO] openmrs-api
[INFO] openmrs-web
[INFO] openmrs-webapp
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building OpenMRS 1.9.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ openmrs ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.1:create (default) @ openmrs ---
[INFO] Checking for local modifications: skipped.
[INFO] Updating project files from SCM: skipped.
[INFO] ShortRevision tag detected. The value is '6'.
[INFO] Executing: /bin/sh -c cd /home/tika/fyp/git/openmrs-core && git rev-parse --verify --short=6 HEAD
[INFO] Working directory: /home/tika/fyp/git/openmrs-core
[INFO] Storing buildNumber: 0 at timestamp: 1369501482170
[INFO] ShortRevision tag detected. The value is '6'.
[INFO] Executing: /bin/sh -c cd /home/tika/fyp/git/openmrs-core && git rev-parse --verify --short=6 HEAD
[INFO] Working directory: /home/tika/fyp/git/openmrs-core
[INFO] Storing buildScmBranch: UNKNOWN_BRANCH
[INFO]
[INFO] --- build-helper-maven-plugin:1.5:parse-version (parse-version) @ openmrs ---
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ openmrs ---
[INFO] Installing /home/tika/fyp/git/openmrs-core/pom.xml to /home/tika/.m2/repository/org/openmrs/openmrs/1.9.4-SNAPSHOT/openmrs-1.9.4-SNAPSHOT.pom
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building openmrs-tools 1.9.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ openmrs-tools ---
[INFO] Deleting /home/tika/fyp/git/openmrs-core/tools/target
[INFO]
[INFO] --- buildnumber-maven-plugin:1.1:create (default) @ openmrs-tools ---
[INFO]
[INFO] --- build-helper-maven-plugin:1.5:parse-version (parse-version) @ openmrs-tools ---
[INFO]
[INFO] --- maven-resources-plugin:2.4:resources (default-resources) @ openmrs-tools ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.1:compile (default-compile) @ openmrs-tools ---
[INFO] Compiling 1 source file to /home/tika/fyp/git/openmrs-core/tools/target/classes
[INFO]
[INFO] --- maven-resources-plugin:2.4:testResources (default-testResources) @ openmrs-tools ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/tika/fyp/git/openmrs-core/tools/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:2.1:testCompile (default-testCompile) @ openmrs-tools ---
[INFO] Not compiling test sources
[INFO]
[INFO] --- maven-surefire-plugin:2.5:test (default-test) @ openmrs-tools ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:2.3.2:jar (default-jar) @ openmrs-tools ---
[INFO] Building jar: /home/tika/fyp/git/openmrs-core/tools/target/openmrs-tools-1.9.4-SNAPSHOT.jar
[INFO]
[INFO] --- maven-jar-plugin:2.3.2:test-jar (default) @ openmrs-tools ---
[INFO] Skipping packaging of the test-jar
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ openmrs-tools ---
[INFO] Installing /home/tika/fyp/git/openmrs-core/tools/target/openmrs-tools-1.9.4-SNAPSHOT.jar to /home/tika/.m2/repository/org/openmrs/tools/openmrs-tools/1.9.4-SNAPSHOT/openmrs-tools-1.9.4-SNAPSHOT.jar
[INFO] Installing /home/tika/fyp/git/openmrs-core/tools/pom.xml to /home/tika/.m2/repository/org/openmrs/tools/openmrs-tools/1.9.4-SNAPSHOT/openmrs-tools-1.9.4-SNAPSHOT.pom
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building openmrs-test 1.9.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ openmrs-test ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.1:create (default) @ openmrs-test ---
[INFO]
[INFO] --- build-helper-maven-plugin:1.5:parse-version (parse-version) @ openmrs-test ---
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ openmrs-test ---
[INFO] Installing /home/tika/fyp/git/openmrs-core/test/pom.xml to /home/tika/.m2/repository/org/openmrs/test/openmrs-test/1.9.4-SNAPSHOT/openmrs-test-1.9.4-SNAPSHOT.pom
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building openmrs-api 1.9.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ openmrs-api ---
[INFO] Deleting /home/tika/fyp/git/openmrs-core/api/target
[INFO]
[INFO] --- buildnumber-maven-plugin:1.1:create (default) @ openmrs-api ---
[INFO]
[INFO] --- build-helper-maven-plugin:1.5:parse-version (parse-version) @ openmrs-api ---
[INFO]
[INFO] --- maven-java-formatter-plugin:0.3:format (default) @ openmrs-api ---
[INFO] Using 'UTF-8' encoding to format source files.
[INFO] Number of files to be formatted: 919
[INFO] Successfully formatted: 0 file(s)
[INFO] Fail to format        : 0 file(s)
[INFO] Skipped               : 919 file(s)
[INFO] Approximate time taken: 5s
[INFO]
[INFO] --- maven-resources-plugin:2.4:resources (default-resources) @ openmrs-api ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 102 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.1:compile (default-compile) @ openmrs-api ---
[INFO] Compiling 699 source files to /home/tika/fyp/git/openmrs-core/api/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] Failure executing javac, but could not parse the error:
An exception has occurred in the compiler (1.6.0_24). Please file a bug at the Java Developer Connection (http://java.sun.com/webapps/bugreport) after checking the Bug Parade for duplicates. Include your program and the following diagnostic in your report. Thank you.
java.lang.NullPointerException
   at com.sun.tools.javac.parser.Parser.block(Parser.java:1497)
   at com.sun.tools.javac.parser.Parser.block(Parser.java:1511)
   at com.sun.tools.javac.parser.Parser.methodDeclaratorRest(Parser.java:2566)
   at com.sun.tools.javac.parser.Parser.classOrInterfaceBodyDeclaration(Parser.java:2515)
   at com.sun.tools.javac.parser.Parser.classOrInterfaceBody(Parser.java:2442)
   at com.sun.tools.javac.parser.Parser.classDeclaration(Parser.java:2287)
   at com.sun.tools.javac.parser.Parser.classOrInterfaceOrEnumDeclaration(Parser.java:2225)
   at com.sun.tools.javac.parser.Parser.typeDeclaration(Parser.java:2214)
   at com.sun.tools.javac.parser.Parser.compilationUnit(Parser.java:2160)
   at com.sun.tools.javac.main.JavaCompiler.parse(JavaCompiler.java:581)
   at com.sun.tools.javac.main.JavaCompiler.parse(JavaCompiler.java:622)
   at com.sun.tools.javac.main.JavaCompiler.parseFiles(JavaCompiler.java:878)
   at com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:796)
   at com.sun.tools.javac.main.Main.compile(Main.java:388)
   at com.sun.tools.javac.main.Main.compile(Main.java:308)
   at com.sun.tools.javac.main.Main.compile(Main.java:299)
   at com.sun.tools.javac.Main.compile(Main.java:100)
   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.compiler.javac.JavacCompiler.compileInProcess(JavacCompiler.java:484)
   at org.codehaus.plexus.compiler.javac.JavacCompiler.compile(JavacCompiler.java:155)
   at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:575)
   at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:116)
   at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
   at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
   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:616)
   at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
   at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
   at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
   at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)

[INFO] 1error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] OpenMRS ........................................... SUCCESS [3.276s]
[INFO] openmrs-tools ..................................... SUCCESS [2.888s]
[INFO] openmrs-test ...................................... SUCCESS [0.048s]
[INFO] openmrs-api ....................................... FAILURE [8.676s]
[INFO] openmrs-web ....................................... SKIPPED
[INFO] openmrs-webapp .................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 15.702s
[INFO] Finished at: Sat May 25 17:04:54 GMT 2013
[INFO] Final Memory: 17M/90M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.1:compile (default-compile) on project openmrs-api: Compilation failure
[ERROR] Failure executing javac, but could not parse the error:
[ERROR] An exception has occurred in the compiler (1.6.0_24). Please file a bug at the Java Developer Connection (http://java.sun.com/webapps/bugreport) after checking the Bug Parade for duplicates. Include your program and the following diagnostic in your report. Thank you.
[ERROR] java.lang.NullPointerException
[ERROR] at com.sun.tools.javac.parser.Parser.block(Parser.java:1497)
[ERROR] at com.sun.tools.javac.parser.Parser.block(Parser.java:1511)
[ERROR] at com.sun.tools.javac.parser.Parser.methodDeclaratorRest(Parser.java:2566)
[ERROR] at com.sun.tools.javac.parser.Parser.classOrInterfaceBodyDeclaration(Parser.java:2515)
[ERROR] at com.sun.tools.javac.parser.Parser.classOrInterfaceBody(Parser.java:2442)
[ERROR] at com.sun.tools.javac.parser.Parser.classDeclaration(Parser.java:2287)
[ERROR] at com.sun.tools.javac.parser.Parser.classOrInterfaceOrEnumDeclaration(Parser.java:2225)
[ERROR] at com.sun.tools.javac.parser.Parser.typeDeclaration(Parser.java:2214)
[ERROR] at com.sun.tools.javac.parser.Parser.compilationUnit(Parser.java:2160)
[ERROR] at com.sun.tools.javac.main.JavaCompiler.parse(JavaCompiler.java:581)
[ERROR] at com.sun.tools.javac.main.JavaCompiler.parse(JavaCompiler.java:622)
[ERROR] at com.sun.tools.javac.main.JavaCompiler.parseFiles(JavaCompiler.java:878)
[ERROR] at com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:796)
[ERROR] at com.sun.tools.javac.main.Main.compile(Main.java:388)
[ERROR] at com.sun.tools.javac.main.Main.compile(Main.java:308)
[ERROR] at com.sun.tools.javac.main.Main.compile(Main.java:299)
[ERROR] at com.sun.tools.javac.Main.compile(Main.java:100)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
[ERROR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ERROR] at java.lang.reflect.Method.invoke(Method.java:616)
[ERROR] at org.codehaus.plexus.compiler.javac.JavacCompiler.compileInProcess(JavacCompiler.java:484)
[ERROR] at org.codehaus.plexus.compiler.javac.JavacCompiler.compile(JavacCompiler.java:155)
[ERROR] at org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:575)
[ERROR] at org.apache.maven.plugin.CompilerMojo.execute(CompilerMojo.java:116)
[ERROR] at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
[ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
[ERROR] at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
[ERROR] at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
[ERROR] at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
[ERROR] at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
[ERROR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ERROR] at java.lang.reflect.Method.invoke(Method.java:616)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:290)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:230)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:409)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:352)
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[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/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :openmrs-api
- Permalink
- 2013-05-25

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user-4ba3b