title: Can't start fresh WSO2-IS install, permission errors
body: <p>I'm having difficulty simply starting WSO2-IS 5.3.0.</p>
  
  <p>Environment : 
  Ubuntu 16.04 VM(Virtualbox) on Ubuntu 16.04 host.</p>
  
  <p>I don't have much additional information, this is a fresh install on a fresh VM. I haven't changed any settings except for what's described in <a href="https://docs.wso2.com/display/IS530/Installing+on+Linux+or+OS+X" rel="nofollow noreferrer">https://docs.wso2.com/display/IS530/Installing+on+Linux+or+OS+X</a></p>
  
  <pre><code>JAVA_HOME environment variable is set to /usr/java/jdk1.8.0_151
  CARBON_HOME environment variable is set to /usr/local/bin/wso2is-5.3.0
  rm: cannot remove '/usr/local/bin/wso2is-5.3.0/tmp/work': Permission denied
  Using Java memory options: -Xms256m -Xmx1024m
  log4j:ERROR setFile(null,true) call failed.
  java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/logs/wso2carbon.log (Permission denied)
      at java.io.FileOutputStream.open0(Native Method)
      at java.io.FileOutputStream.open(FileOutputStream.java:270)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:213)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:133)
      at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
      at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
      at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:223)
      at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
      at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
      at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
      at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
      at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
      at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:648)
      at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:514)
      at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
      at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
      at org.apache.log4j.LogManager.&lt;clinit&gt;(LogManager.java:127)
      at org.apache.log4j.Logger.getLogger(Logger.java:104)
      at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:262)
      at org.apache.commons.logging.impl.Log4JLogger.&lt;init&gt;(Log4JLogger.java:108)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1025)
      at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:844)
      at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:541)
      at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:292)
      at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:269)
      at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:655)
      at org.wso2.carbon.server.Main.&lt;clinit&gt;(Main.java:34)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at java.lang.Class.newInstance(Class.java:442)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:60)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  log4j:ERROR Either File or DatePattern options are not set for appender [CARBON_LOGFILE].
  log4j:ERROR setFile(null,true) call failed.
  java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/logs/patches.log (Permission denied)
      at java.io.FileOutputStream.open0(Native Method)
      at java.io.FileOutputStream.open(FileOutputStream.java:270)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:213)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:133)
      at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
      at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
      at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
      at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
      at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
      at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
      at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
      at org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)
      at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)
      at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
      at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
      at org.apache.log4j.LogManager.&lt;clinit&gt;(LogManager.java:127)
      at org.apache.log4j.Logger.getLogger(Logger.java:104)
      at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:262)
      at org.apache.commons.logging.impl.Log4JLogger.&lt;init&gt;(Log4JLogger.java:108)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1025)
      at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:844)
      at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:541)
      at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:292)
      at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:269)
      at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:655)
      at org.wso2.carbon.server.Main.&lt;clinit&gt;(Main.java:34)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at java.lang.Class.newInstance(Class.java:442)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:60)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  log4j:ERROR setFile(null,true) call failed.
  java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/logs/wso2carbon-trace-messages.log (Permission denied)
      at java.io.FileOutputStream.open0(Native Method)
      at java.io.FileOutputStream.open(FileOutputStream.java:270)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:213)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:133)
      at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
      at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
      at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:223)
      at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
      at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
      at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
      at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
      at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
      at org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)
      at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)
      at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
      at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
      at org.apache.log4j.LogManager.&lt;clinit&gt;(LogManager.java:127)
      at org.apache.log4j.Logger.getLogger(Logger.java:104)
      at org.apache.commons.logging.impl.Log4JLogger.getLogger(Log4JLogger.java:262)
      at org.apache.commons.logging.impl.Log4JLogger.&lt;init&gt;(Log4JLogger.java:108)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at org.apache.commons.logging.impl.LogFactoryImpl.createLogFromClass(LogFactoryImpl.java:1025)
      at org.apache.commons.logging.impl.LogFactoryImpl.discoverLogImplementation(LogFactoryImpl.java:844)
      at org.apache.commons.logging.impl.LogFactoryImpl.newInstance(LogFactoryImpl.java:541)
      at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:292)
      at org.apache.commons.logging.impl.LogFactoryImpl.getInstance(LogFactoryImpl.java:269)
      at org.apache.commons.logging.LogFactory.getLog(LogFactory.java:655)
      at org.wso2.carbon.server.Main.&lt;clinit&gt;(Main.java:34)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at java.lang.Class.newInstance(Class.java:442)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:60)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  log4j:ERROR Either File or DatePattern options are not set for appender [CARBON_TRACE_LOGFILE].
  [2017-11-22 17:16:33,708]  WARN {org.wso2.carbon.server.Main} -  Cannot write wso2carbon.pid file
  [2017-11-22 17:16:33,713] ERROR {org.wso2.carbon.server.extensions.FragmentBundleCreator} -  Error occured while creating the log4j prop fragment bundle.
  java.io.IOException: Fail to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/jarsToBundles
      at org.wso2.carbon.server.util.Utils.copyFileToDir(Utils.java:494)
      at org.wso2.carbon.server.extensions.FragmentBundleCreator.perform(FragmentBundleCreator.java:70)
      at org.wso2.carbon.server.Main.invokeExtensions(Main.java:142)
      at org.wso2.carbon.server.Main.main(Main.java:92)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  [2017-11-22 17:16:33,732] ERROR {org.wso2.carbon.server.extensions.DropinsBundleDeployer} -  Failed to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/bundles_info_bcd7eb77-3295-4fac-8942-a5cde9d32434/bundles.info
  java.io.IOException: Failed to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/bundles_info_bcd7eb77-3295-4fac-8942-a5cde9d32434/bundles.info
      at org.wso2.carbon.server.extensions.DropinsBundleDeployer.updateBundlesInfoFile(DropinsBundleDeployer.java:323)
      at org.wso2.carbon.server.extensions.DropinsBundleDeployer.perform(DropinsBundleDeployer.java:87)
      at org.wso2.carbon.server.Main.invokeExtensions(Main.java:146)
      at org.wso2.carbon.server.Main.main(Main.java:92)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  [2017-11-22 17:16:33,732] ERROR {org.wso2.carbon.server.extensions.DropinsBundleDeployer} -  Error occured while deploying bundles in the dropins directory
  java.lang.Exception: Error occurred while updating the bundles.info file.
      at org.wso2.carbon.server.extensions.DropinsBundleDeployer.updateBundlesInfoFile(DropinsBundleDeployer.java:345)
      at org.wso2.carbon.server.extensions.DropinsBundleDeployer.perform(DropinsBundleDeployer.java:87)
      at org.wso2.carbon.server.Main.invokeExtensions(Main.java:146)
      at org.wso2.carbon.server.Main.main(Main.java:92)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  Caused by: java.io.IOException: Failed to create the directory: /usr/local/bin/wso2is-5.3.0/tmp/bundles_info_bcd7eb77-3295-4fac-8942-a5cde9d32434/bundles.info
      at org.wso2.carbon.server.extensions.DropinsBundleDeployer.updateBundlesInfoFile(DropinsBundleDeployer.java:323)
      ... 9 more
  [2017-11-22 17:16:33,735] ERROR {org.wso2.carbon.server.extensions.PatchInstaller} -  Error occurred while applying patches
  java.io.IOException: No such file or directory
      at java.io.UnixFileSystem.createFileExclusively(Native Method)
      at java.io.File.createNewFile(File.java:1012)
      at org.wso2.carbon.server.util.PatchUtils.processPatches(PatchUtils.java:218)
      at org.wso2.carbon.server.extensions.PatchInstaller.perform(PatchInstaller.java:49)
      at org.wso2.carbon.server.Main.invokeExtensions(Main.java:149)
      at org.wso2.carbon.server.Main.main(Main.java:92)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  [2017-11-22 17:16:33,736] ERROR {org.wso2.carbon.server.extensions.EclipseIniRewriter} -  Error while writing to file null.ini
  java.io.FileNotFoundException: /usr/local/bin/wso2is-5.3.0/repository/components/default/null.ini (Permission denied)
      at java.io.FileOutputStream.open0(Native Method)
      at java.io.FileOutputStream.open(FileOutputStream.java:270)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:213)
      at java.io.FileOutputStream.&lt;init&gt;(FileOutputStream.java:162)
      at java.io.FileWriter.&lt;init&gt;(FileWriter.java:90)
      at org.wso2.carbon.server.extensions.EclipseIniRewriter.rewriteFile(EclipseIniRewriter.java:73)
      at org.wso2.carbon.server.extensions.EclipseIniRewriter.perform(EclipseIniRewriter.java:55)
      at org.wso2.carbon.server.Main.invokeExtensions(Main.java:152)
      at org.wso2.carbon.server.Main.main(Main.java:92)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  !SESSION 2017-11-22 17:16:33.950 -----------------------------------------------
  eclipse.buildId=unknown
  java.version=1.8.0_151
  java.vendor=Oracle Corporation
  BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
  
  !ENTRY org.eclipse.osgi 4 0 2017-11-22 17:16:33.950
  !MESSAGE Error reading configuration: Unable to create lock manager.
  !STACK 0
  java.io.IOException: Unable to create lock manager.
      at org.eclipse.osgi.storagemanager.StorageManager.open(StorageManager.java:699)
      at org.eclipse.osgi.internal.baseadaptor.BaseStorage.initFileManager(BaseStorage.java:226)
      at org.eclipse.osgi.internal.baseadaptor.BaseStorage.initialize(BaseStorage.java:160)
      at org.eclipse.osgi.baseadaptor.BaseAdaptor.initializeStorage(BaseAdaptor.java:123)
      at org.eclipse.osgi.framework.internal.core.Framework.&lt;init&gt;(Framework.java:192)
      at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(EclipseStarter.java:263)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.server.CarbonLauncher.launch(CarbonLauncher.java:108)
      at org.wso2.carbon.server.Main.launchCarbon(Main.java:160)
      at org.wso2.carbon.server.Main.main(Main.java:94)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at org.wso2.carbon.bootstrap.Bootstrap.loadClass(Bootstrap.java:63)
      at org.wso2.carbon.bootstrap.Bootstrap.main(Bootstrap.java:45)
  </code></pre>