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iPlantCollaborativeOpenSource / TNRS

The Taxonomic Name Resolution Service is a free utility for correcting and standardizing plant names.
http://tnrs.iplantcollaborative.org
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Errors during INSTALL #2

Closed cmonnom closed 11 years ago

cmonnom commented 11 years ago

a. Create the TNRS system user. useradd tnrs -g tnrs -c 'TNRS services'

useradd: group 'tnrs' does not exist

d. Create the configuration directory. mkdir /home/tnrs/.tnrs cp ~/TNRS/config/tnrs.properties /home/tnrs/.tnrs/ chown -R tnrs:tnrs /home/tnrs/.tnrs

mkdir: cannot create directory `/home/tnrs/.tnrs': No such file or directory

a. Use Apache Maven to build the service. cd ~/TNRS/tnrs-services mvn clean compile package

[INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.iplantc.tnrs:tnrsservices:jar:1.0-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 94, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-surefire-plugin is missing. @ line 113, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-idea-plugin is missing. @ line 122, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-compiler-plugin is missing. @ line 130, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ line 139, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-surefire-report-plugin is missing. @ line 146, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-pmd-plugin is missing. @ line 151, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.codehaus.mojo:cobertura-maven-plugin is missing. @ line 158, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.codehaus.mojo:taglist-maven-plugin is missing. @ line 162, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-jxr-plugin is missing. @ line 175, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.apache.maven.plugins:maven-javadoc-plugin is missing. @ line 179, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.codehaus.mojo:jdepend-maven-plugin is missing. @ line 191, column 12 [WARNING] 'reporting.plugins.plugin.version' for org.codehaus.mojo:findbugs-maven-plugin is missing. @ line 195, 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]

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T E S T S

Running org.iplantc.tnrs.TnrsservicesTestCase org.apache.maven.surefire.booter.SurefireExecutionException: org.iplantc.tnrs.TnrsservicesTestCase; nested exception is java.lang.IllegalAccessError: tried to access method org.apache.log4j.Logger.(Ljava/lang/String;)V from class org.apache.log4j.spi.RootLogger; nested exception is org.apache.maven.surefire.testset.TestSetFailedException: org.iplantc.tnrs.TnrsservicesTestCase; nested exception is java.lang.IllegalAccessError: tried to access method org.apache.log4j.Logger.(Ljava/lang/String;)V from class org.apache.log4j.spi.RootLogger org.apache.maven.surefire.testset.TestSetFailedException: org.iplantc.tnrs.TnrsservicesTestCase; nested exception is java.lang.IllegalAccessError: tried to access method org.apache.log4j.Logger.(Ljava/lang/String;)V from class org.apache.log4j.spi.RootLogger java.lang.IllegalAccessError: tried to access method org.apache.log4j.Logger.(Ljava/lang/String;)V from class org.apache.log4j.spi.RootLogger at org.apache.log4j.spi.RootLogger.(RootLogger.java:43) at org.apache.log4j.LogManager.(LogManager.java:78) at org.slf4j.impl.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:73) at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:88) at org.apache.commons.logging.impl.SLF4JLogFactory.getInstance(SLF4JLogFactory.java:155) at org.apache.commons.logging.impl.SLF4JLogFactory.getInstance(SLF4JLogFactory.java:131) at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:685) at org.mule.util.SystemUtils.(SystemUtils.java:34) at org.mule.tck.AbstractMuleTestCase.(AbstractMuleTestCase.java:115) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:525) at junit.framework.TestSuite.createTest(TestSuite.java:54) at junit.framework.TestSuite.addTestMethod(TestSuite.java:280) at junit.framework.TestSuite.(TestSuite.java:140) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:525) at org.apache.maven.surefire.junit.JUnitTestSet.constructTestObject(JUnitTestSet.java:151) at org.apache.maven.surefire.junit.JUnitTestSet.execute(JUnitTestSet.java:197) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.executeTestSet(AbstractDirectoryTestSuite.java:115) at org.apache.maven.surefire.suite.AbstractDirectoryTestSuite.execute(AbstractDirectoryTestSuite.java:102) at org.apache.maven.surefire.Surefire.run(Surefire.java:180) 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:601) at org.apache.maven.surefire.booter.SurefireBooter.runSuitesInProcess(SurefireBooter.java:350) at org.apache.maven.surefire.booter.SurefireBooter.main(SurefireBooter.java:1021) [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 17.375s [INFO] Finished at: Tue Feb 19 15:25:35 UTC 2013 [INFO] Final Memory: 26M/63M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.5:test (default-test) on project tnrsservices: There are test failures. [ERROR] [ERROR] Please refer to /root/TNRS/tnrs-services/target/surefire-reports for the individual test results. [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