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https://issues.apache.org/jira/browse/HDFS-4063?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Steve Loughran reopened HDFS-4063:
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reopening as it isn't fixed until the patch is checked in.

                
> Unable to change JAVA_HOME directory in hadoop-setup-conf.sh script.
> --------------------------------------------------------------------
>
>                 Key: HDFS-4063
>                 URL: https://issues.apache.org/jira/browse/HDFS-4063
>             Project: Hadoop HDFS
>          Issue Type: Bug
>          Components: scripts, tools
>    Affects Versions: 1.0.3
>         Environment: Fedora 17 3.3.4-5.fc17.x86_64t, java version 
> "1.7.0_06-icedtea", Rackspace Cloud (NextGen)
>            Reporter: Haoquan Wang
>            Priority: Minor
>              Labels: patch
>             Fix For: 1.0.3
>
>   Original Estimate: 1h
>  Remaining Estimate: 1h
>
> The JAVA_HOME directory remains unchanged no matter what you enter when you 
> run hadoop-setup-conf.sh to generate hadoop configurations. Please see below 
> example:
> *********************************************************
> [root@hadoop-slave ~]# /sbin/hadoop-setup-conf.sh
> Setup Hadoop Configuration
> Where would you like to put config directory? (/etc/hadoop)
> Where would you like to put log directory? (/var/log/hadoop)
> Where would you like to put pid directory? (/var/run/hadoop)
> What is the host of the namenode? (hadoop-slave)
> Where would you like to put namenode data directory? 
> (/var/lib/hadoop/hdfs/namenode)
> Where would you like to put datanode data directory? 
> (/var/lib/hadoop/hdfs/datanode)
> What is the host of the jobtracker? (hadoop-slave)
> Where would you like to put jobtracker/tasktracker data directory? 
> (/var/lib/hadoop/mapred)
> Where is JAVA_HOME directory? (/usr/java/default) *+/usr/lib/jvm/jre+*
> Would you like to create directories/copy conf files to localhost? (Y/n)
> Review your choices:
> Config directory            : /etc/hadoop
> Log directory               : /var/log/hadoop
> PID directory               : /var/run/hadoop
> Namenode host               : hadoop-slave
> Namenode directory          : /var/lib/hadoop/hdfs/namenode
> Datanode directory          : /var/lib/hadoop/hdfs/datanode
> Jobtracker host             : hadoop-slave
> Mapreduce directory         : /var/lib/hadoop/mapred
> Task scheduler              : org.apache.hadoop.mapred.JobQueueTaskScheduler
> JAVA_HOME directory         : *+/usr/java/default+*
> Create dirs/copy conf files : y
> Proceed with generate configuration? (y/N) n
> User aborted setup, exiting...
> *********************************************************
> Resolution:
> Amend line 509 in file /sbin/hadoop-setup-conf.sh
> from:
> JAVA_HOME=${USER_USER_JAVA_HOME:-$JAVA_HOME}
> to:
> JAVA_HOME=${USER_JAVA_HOME:-$JAVA_HOME}
> will resolve this issue.

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