[BioMart Users] svn update for rc3 get compiler error when run ant

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[BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
svn update for rc3 get compiler error when run ant

Hi,

Im trying to upgrade my RC3 installation to the new RC3 code that fixes the copy/paste URL bug. I ran

svn update

ant

When I ran ant, I received the following compiler error:

      Buildfile: build.xml

      -load.properties:

      -init:

      compile.main:

          [javac] Compiling 114 source files to /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main

          [javac] ----------

          [javac] 1. ERROR in /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/utils/McGuiUtils.java (at line 1)

          [javac]     package org.biomart.configurator.utils;

          [javac]     ^^

          [javac] The type Enum is not generic; it cannot be parameterized with arguments <McGuiUtils>

          [javac] ----------

          [javac] 1 problem (1 error)

      BUILD FAILED

      /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile failed; see the compiler error output for details.

This is the portion of the McGuiType.java script that is having issues

      /**

       * this class should not be used for web, should only be used for

       * MartConfigurator GUI.

       */

      public enum McGuiUtils {

              INSTANCE;

              private McGuiType guiType;

What am I missing?

Thanks,

Heather


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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
Heather,

try:
   ant clean
and then
   ant

also, please make sure you are running the above commands from the
following directory:

/lscratch/apps/BioMart8/trunk_jan_26/trunk/

thanks
Syed

On 09/02/2011 23:36, Estrella, Heather wrote:

> Hi,
>
> I’m trying to upgrade my RC3 installation to the new RC3 code that fixes the copy/paste URL bug. I ran
>
> svn update
>
> ant
>
> When I ran ant, I received the following compiler error:
>
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>
> compile.main:
>
>      [javac] Compiling 114 source files to /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>
>      [javac] ----------
>
>      [javac] 1. ERROR in /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/utils/McGuiUtils.java (at line 1)
>
>      [javac]     package org.biomart.configurator.utils;
>
>      [javac]     ^^
>
>      [javac] The type Enum is not generic; it cannot be parameterized with arguments<McGuiUtils>
>
>      [javac] ----------
>
>      [javac] 1 problem (1 error)
>
> BUILD FAILED
>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile failed; see the compiler error output for details.
>
> This is the portion of the McGuiType.java script that is having issues
>
> …
>
> /**
>
>   * this class should not be used for web, should only be used for
>
>   * MartConfigurator GUI.
>
>   */
>
> public enum McGuiUtils {
>
>          INSTANCE;
>
>          private McGuiType guiType;
>
> …
>
> What am I missing?
>
> Thanks,
>
> Heather
>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
Thanks Syed,

That got me past the ant problem. However, it looks like running svn
update automatically took my rc3 code to rc4.

I'm trying to start my biomart server back up using "
./scripts/biomart-server.sh start" and I get the following error:
        ** ERROR:
/lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
readable!

This jar file doesn't exist in the scripts directory. It isn't found
anywhere in the installation path.

Here is a list of what is in the scripts directory:
biomart-server.bat  
build.sh  
fasta.sh              
jetty.bat          
Jetty-Service.exe  
martconfigurator.bat  
martrunner.bat  
prunmgr.exe  
runSoakTest.sh
biomart-server.sh  
fasta.bat  
generate-password.sh
jetty-service.conf  
launch.sh        
martconfigurator.sh  
martrunner.sh  
prunsrv.exe  
test.sh

Also, can you please point me to the documentation is located? I'm kinda
running blind.

Thanks,
Heather

-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 3:47 PM
To: Estrella, Heather
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

Heather,

try:
   ant clean
and then
   ant

also, please make sure you are running the above commands from the
following directory:

/lscratch/apps/BioMart8/trunk_jan_26/trunk/

thanks
Syed

On 09/02/2011 23:36, Estrella, Heather wrote:
> Hi,
>
> I'm trying to upgrade my RC3 installation to the new RC3 code that
fixes the copy/paste URL bug. I ran

>
> svn update
>
> ant
>
> When I ran ant, I received the following compiler error:
>
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>
> compile.main:
>
>      [javac] Compiling 114 source files to
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>
>      [javac] ----------
>
>      [javac] 1. ERROR in
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
utils/McGuiUtils.java (at line 1)
>
>      [javac]     package org.biomart.configurator.utils;
>
>      [javac]     ^^
>
>      [javac] The type Enum is not generic; it cannot be parameterized
with arguments<McGuiUtils>
>
>      [javac] ----------
>
>      [javac] 1 problem (1 error)
>
> BUILD FAILED
>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
failed; see the compiler error output for details.

>
> This is the portion of the McGuiType.java script that is having issues
>
> ...
>
> /**
>
>   * this class should not be used for web, should only be used for
>
>   * MartConfigurator GUI.
>
>   */
>
> public enum McGuiUtils {
>
>          INSTANCE;
>
>          private McGuiType guiType;
>
> ...
>
> What am I missing?
>
> Thanks,
>
> Heather
>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
Heather,

1- please send me the console output when you run 'ant'

2- to start/stop biomart server, the commands are:

./dist/scripts/biomart-server.sh stop
./dist/scripts/biomart-server.sh start

thats from the dist directory. let me know if that helps.

Syed

On 09/02/2011 23:56, Estrella, Heather wrote:

> Thanks Syed,
>
> That got me past the ant problem. However, it looks like running svn
> update automatically took my rc3 code to rc4.
>
> I'm trying to start my biomart server back up using "
> ./scripts/biomart-server.sh start" and I get the following error:
> ** ERROR:
> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
> readable!
>
> This jar file doesn't exist in the scripts directory. It isn't found
> anywhere in the installation path.
>
> Here is a list of what is in the scripts directory:
> biomart-server.bat
> build.sh
> fasta.sh
> jetty.bat
> Jetty-Service.exe
> martconfigurator.bat
> martrunner.bat
> prunmgr.exe
> runSoakTest.sh
> biomart-server.sh
> fasta.bat
> generate-password.sh
> jetty-service.conf
> launch.sh
> martconfigurator.sh
> martrunner.sh
> prunsrv.exe
> test.sh
>
> Also, can you please point me to the documentation is located? I'm kinda
> running blind.
>
> Thanks,
> Heather
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 3:47 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
> run ant
>
> Heather,
>
> try:
>     ant clean
> and then
>     ant
>
> also, please make sure you are running the above commands from the
> following directory:
>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>
> thanks
> Syed
>
> On 09/02/2011 23:36, Estrella, Heather wrote:
>> Hi,
>>
>> I'm trying to upgrade my RC3 installation to the new RC3 code that
> fixes the copy/paste URL bug. I ran
>>
>> svn update
>>
>> ant
>>
>> When I ran ant, I received the following compiler error:
>>
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> -init:
>>
>> compile.main:
>>
>>       [javac] Compiling 114 source files to
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>
>>       [javac] ----------
>>
>>       [javac] 1. ERROR in
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
> utils/McGuiUtils.java (at line 1)
>>
>>       [javac]     package org.biomart.configurator.utils;
>>
>>       [javac]     ^^
>>
>>       [javac] The type Enum is not generic; it cannot be parameterized
> with arguments<McGuiUtils>
>>
>>       [javac] ----------
>>
>>       [javac] 1 problem (1 error)
>>
>> BUILD FAILED
>>
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
> failed; see the compiler error output for details.
>>
>> This is the portion of the McGuiType.java script that is having issues
>>
>> ...
>>
>> /**
>>
>>    * this class should not be used for web, should only be used for
>>
>>    * MartConfigurator GUI.
>>
>>    */
>>
>> public enum McGuiUtils {
>>
>>           INSTANCE;
>>
>>           private McGuiType guiType;
>>
>> ...
>>
>> What am I missing?
>>
>> Thanks,
>>
>> Heather
>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
Thanks Syed,

When I ran the 'ant clean' the first time, it deleted the dist directory
and the only place I could find the biomart-server.sh script is now in
the scripts directory located at $BIOMART_HOME

bash-3.2$ ant clean
Buildfile: build.xml

-load.properties:

clean:

BUILD SUCCESSFUL
Total time: 0 seconds

Here's a list of the BIOMART_HOME directory contents. "ant clean" really
changed the directory structure from what I was previously used to (i.e.
dist/scripts, etc.). because there is now a "plugins" directory is why I
thought maybe "svn update" updated my original rc3 installation to rc4.
However, even in the rc4 install that we have, there is still the dist
directory so I don't know what's going on.
ant.properties  
build_test.xml  
build.xml  
conf  
ext  
images  
lib  
plugins  
registry  
scripts  
src  
start  
test  
testdata  
voldemort  
web



-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 4:08 PM
To: Estrella, Heather
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

Heather,

1- please send me the console output when you run 'ant'

2- to start/stop biomart server, the commands are:

./dist/scripts/biomart-server.sh stop
./dist/scripts/biomart-server.sh start

thats from the dist directory. let me know if that helps.

Syed

On 09/02/2011 23:56, Estrella, Heather wrote:

> Thanks Syed,
>
> That got me past the ant problem. However, it looks like running svn
> update automatically took my rc3 code to rc4.
>
> I'm trying to start my biomart server back up using "
> ./scripts/biomart-server.sh start" and I get the following error:
> ** ERROR:
> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
> readable!
>
> This jar file doesn't exist in the scripts directory. It isn't found
> anywhere in the installation path.
>
> Here is a list of what is in the scripts directory:
> biomart-server.bat
> build.sh
> fasta.sh
> jetty.bat
> Jetty-Service.exe
> martconfigurator.bat
> martrunner.bat
> prunmgr.exe
> runSoakTest.sh
> biomart-server.sh
> fasta.bat
> generate-password.sh
> jetty-service.conf
> launch.sh
> martconfigurator.sh
> martrunner.sh
> prunsrv.exe
> test.sh
>
> Also, can you please point me to the documentation is located? I'm
kinda

> running blind.
>
> Thanks,
> Heather
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 3:47 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
when

> run ant
>
> Heather,
>
> try:
>     ant clean
> and then
>     ant
>
> also, please make sure you are running the above commands from the
> following directory:
>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>
> thanks
> Syed
>
> On 09/02/2011 23:36, Estrella, Heather wrote:
>> Hi,
>>
>> I'm trying to upgrade my RC3 installation to the new RC3 code that
> fixes the copy/paste URL bug. I ran
>>
>> svn update
>>
>> ant
>>
>> When I ran ant, I received the following compiler error:
>>
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> -init:
>>
>> compile.main:
>>
>>       [javac] Compiling 114 source files to
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>
>>       [javac] ----------
>>
>>       [javac] 1. ERROR in
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
> utils/McGuiUtils.java (at line 1)
>>
>>       [javac]     package org.biomart.configurator.utils;
>>
>>       [javac]     ^^
>>
>>       [javac] The type Enum is not generic; it cannot be
parameterized

> with arguments<McGuiUtils>
>>
>>       [javac] ----------
>>
>>       [javac] 1 problem (1 error)
>>
>> BUILD FAILED
>>
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
> failed; see the compiler error output for details.
>>
>> This is the portion of the McGuiType.java script that is having
issues

>>
>> ...
>>
>> /**
>>
>>    * this class should not be used for web, should only be used for
>>
>>    * MartConfigurator GUI.
>>
>>    */
>>
>> public enum McGuiUtils {
>>
>>           INSTANCE;
>>
>>           private McGuiType guiType;
>>
>> ...
>>
>> What am I missing?
>>
>> Thanks,
>>
>> Heather
>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
In reply to this post by Estrella, Heather
Oh, and the documentation:

for rc3:
http://www.biomart.org/rc3_documentation.pdf

for rc4:
http://www.biomart.org/rc4_documentation.pdf

Best,
Syed

On 09/02/2011 23:56, Estrella, Heather wrote:

> Thanks Syed,
>
> That got me past the ant problem. However, it looks like running svn
> update automatically took my rc3 code to rc4.
>
> I'm trying to start my biomart server back up using "
> ./scripts/biomart-server.sh start" and I get the following error:
> ** ERROR:
> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
> readable!
>
> This jar file doesn't exist in the scripts directory. It isn't found
> anywhere in the installation path.
>
> Here is a list of what is in the scripts directory:
> biomart-server.bat
> build.sh
> fasta.sh
> jetty.bat
> Jetty-Service.exe
> martconfigurator.bat
> martrunner.bat
> prunmgr.exe
> runSoakTest.sh
> biomart-server.sh
> fasta.bat
> generate-password.sh
> jetty-service.conf
> launch.sh
> martconfigurator.sh
> martrunner.sh
> prunsrv.exe
> test.sh
>
> Also, can you please point me to the documentation is located? I'm kinda
> running blind.
>
> Thanks,
> Heather
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 3:47 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
> run ant
>
> Heather,
>
> try:
>     ant clean
> and then
>     ant
>
> also, please make sure you are running the above commands from the
> following directory:
>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>
> thanks
> Syed
>
> On 09/02/2011 23:36, Estrella, Heather wrote:
>> Hi,
>>
>> I'm trying to upgrade my RC3 installation to the new RC3 code that
> fixes the copy/paste URL bug. I ran
>>
>> svn update
>>
>> ant
>>
>> When I ran ant, I received the following compiler error:
>>
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> -init:
>>
>> compile.main:
>>
>>       [javac] Compiling 114 source files to
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>
>>       [javac] ----------
>>
>>       [javac] 1. ERROR in
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
> utils/McGuiUtils.java (at line 1)
>>
>>       [javac]     package org.biomart.configurator.utils;
>>
>>       [javac]     ^^
>>
>>       [javac] The type Enum is not generic; it cannot be parameterized
> with arguments<McGuiUtils>
>>
>>       [javac] ----------
>>
>>       [javac] 1 problem (1 error)
>>
>> BUILD FAILED
>>
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
> failed; see the compiler error output for details.
>>
>> This is the portion of the McGuiType.java script that is having issues
>>
>> ...
>>
>> /**
>>
>>    * this class should not be used for web, should only be used for
>>
>>    * MartConfigurator GUI.
>>
>>    */
>>
>> public enum McGuiUtils {
>>
>>           INSTANCE;
>>
>>           private McGuiType guiType;
>>
>> ...
>>
>> What am I missing?
>>
>> Thanks,
>>
>> Heather
>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
In reply to this post by Estrella, Heather
You need to run:

ant

after ant clean.

then it will recreate the dist/

and then run:

./dist/scripts/biomart-server.sh start




On 10/02/2011 00:07, Estrella, Heather wrote:

> Thanks Syed,
>
> When I ran the 'ant clean' the first time, it deleted the dist directory
> and the only place I could find the biomart-server.sh script is now in
> the scripts directory located at $BIOMART_HOME
>
> bash-3.2$ ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>
> BUILD SUCCESSFUL
> Total time: 0 seconds
>
> Here's a list of the BIOMART_HOME directory contents. "ant clean" really
> changed the directory structure from what I was previously used to (i.e.
> dist/scripts, etc.). because there is now a "plugins" directory is why I
> thought maybe "svn update" updated my original rc3 installation to rc4.
> However, even in the rc4 install that we have, there is still the dist
> directory so I don't know what's going on.
> ant.properties
> build_test.xml
> build.xml
> conf
> ext
> images
> lib
> plugins
> registry
> scripts
> src
> start
> test
> testdata
> voldemort
> web
>
>
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:08 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
> run ant
>
> Heather,
>
> 1- please send me the console output when you run 'ant'
>
> 2- to start/stop biomart server, the commands are:
>
> ./dist/scripts/biomart-server.sh stop
> ./dist/scripts/biomart-server.sh start
>
> thats from the dist directory. let me know if that helps.
>
> Syed
>
> On 09/02/2011 23:56, Estrella, Heather wrote:
>> Thanks Syed,
>>
>> That got me past the ant problem. However, it looks like running svn
>> update automatically took my rc3 code to rc4.
>>
>> I'm trying to start my biomart server back up using "
>> ./scripts/biomart-server.sh start" and I get the following error:
>> ** ERROR:
>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>> readable!
>>
>> This jar file doesn't exist in the scripts directory. It isn't found
>> anywhere in the installation path.
>>
>> Here is a list of what is in the scripts directory:
>> biomart-server.bat
>> build.sh
>> fasta.sh
>> jetty.bat
>> Jetty-Service.exe
>> martconfigurator.bat
>> martrunner.bat
>> prunmgr.exe
>> runSoakTest.sh
>> biomart-server.sh
>> fasta.bat
>> generate-password.sh
>> jetty-service.conf
>> launch.sh
>> martconfigurator.sh
>> martrunner.sh
>> prunsrv.exe
>> test.sh
>>
>> Also, can you please point me to the documentation is located? I'm
> kinda
>> running blind.
>>
>> Thanks,
>> Heather
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 3:47 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> Heather,
>>
>> try:
>>      ant clean
>> and then
>>      ant
>>
>> also, please make sure you are running the above commands from the
>> following directory:
>>
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>
>> thanks
>> Syed
>>
>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>> Hi,
>>>
>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>> fixes the copy/paste URL bug. I ran
>>>
>>> svn update
>>>
>>> ant
>>>
>>> When I ran ant, I received the following compiler error:
>>>
>>> Buildfile: build.xml
>>>
>>> -load.properties:
>>>
>>> -init:
>>>
>>> compile.main:
>>>
>>>        [javac] Compiling 114 source files to
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>
>>>        [javac] ----------
>>>
>>>        [javac] 1. ERROR in
>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
>> utils/McGuiUtils.java (at line 1)
>>>
>>>        [javac]     package org.biomart.configurator.utils;
>>>
>>>        [javac]     ^^
>>>
>>>        [javac] The type Enum is not generic; it cannot be
> parameterized
>> with arguments<McGuiUtils>
>>>
>>>        [javac] ----------
>>>
>>>        [javac] 1 problem (1 error)
>>>
>>> BUILD FAILED
>>>
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>> failed; see the compiler error output for details.
>>>
>>> This is the portion of the McGuiType.java script that is having
> issues
>>>
>>> ...
>>>
>>> /**
>>>
>>>     * this class should not be used for web, should only be used for
>>>
>>>     * MartConfigurator GUI.
>>>
>>>     */
>>>
>>> public enum McGuiUtils {
>>>
>>>            INSTANCE;
>>>
>>>            private McGuiType guiType;
>>>
>>> ...
>>>
>>> What am I missing?
>>>
>>> Thanks,
>>>
>>> Heather
>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
I just get the Enum error. I just tried re-downloading a clean version
of rc4 to see if I can get that to run a little more smoothly. The
install that we had is pretty much messed up until the java compilation
error is resolved.

Here's the exact sequence of commands I've run:

svn update
ant clean
ant

I've tried re-running them in that sequence and here's the output:

-bash-3.2$ svn update
        At revision 7145.

-bash-3.2$ ant clean
        Buildfile: build.xml

        -load.properties:

        clean:
           [delete] Deleting directory
/lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
           [delete] Deleting directory
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build

        BUILD SUCCESSFUL
       
-bash-3.2$ ant
        Buildfile: build.xml

        -load.properties:

        -init:
            [mkdir] Created dir:
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
            [mkdir] Created dir:
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
            [mkdir] Created dir:
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
            [mkdir] Created dir:
/lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
            [mkdir] Created dir:
/lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
            [mkdir] Created dir:
/lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices

        compile.main:
            [javac] Compiling 455 source files to
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
            [javac] ----------
            [javac] 1. ERROR in
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope
ration.java (at line 1)
            [javac]     package org.biomart.api.enums;
            [javac]     ^^
            [javac] The type Enum is not generic; it cannot be
parameterized with arguments <Operation>
            [javac] ----------
       
            [javac] 1 problem (1 error)

        BUILD FAILED
        /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
failed; see the compiler error output for details.

        Total time: 1 second


-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 4:16 PM
To: Estrella, Heather
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

You need to run:

ant

after ant clean.

then it will recreate the dist/

and then run:

./dist/scripts/biomart-server.sh start




On 10/02/2011 00:07, Estrella, Heather wrote:
> Thanks Syed,
>
> When I ran the 'ant clean' the first time, it deleted the dist
directory

> and the only place I could find the biomart-server.sh script is now in
> the scripts directory located at $BIOMART_HOME
>
> bash-3.2$ ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>
> BUILD SUCCESSFUL
> Total time: 0 seconds
>
> Here's a list of the BIOMART_HOME directory contents. "ant clean"
really
> changed the directory structure from what I was previously used to
(i.e.
> dist/scripts, etc.). because there is now a "plugins" directory is why
I
> thought maybe "svn update" updated my original rc3 installation to
rc4.

> However, even in the rc4 install that we have, there is still the dist
> directory so I don't know what's going on.
> ant.properties
> build_test.xml
> build.xml
> conf
> ext
> images
> lib
> plugins
> registry
> scripts
> src
> start
> test
> testdata
> voldemort
> web
>
>
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:08 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
when

> run ant
>
> Heather,
>
> 1- please send me the console output when you run 'ant'
>
> 2- to start/stop biomart server, the commands are:
>
> ./dist/scripts/biomart-server.sh stop
> ./dist/scripts/biomart-server.sh start
>
> thats from the dist directory. let me know if that helps.
>
> Syed
>
> On 09/02/2011 23:56, Estrella, Heather wrote:
>> Thanks Syed,
>>
>> That got me past the ant problem. However, it looks like running svn
>> update automatically took my rc3 code to rc4.
>>
>> I'm trying to start my biomart server back up using "
>> ./scripts/biomart-server.sh start" and I get the following error:
>> ** ERROR:
>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>> readable!
>>
>> This jar file doesn't exist in the scripts directory. It isn't found
>> anywhere in the installation path.
>>
>> Here is a list of what is in the scripts directory:
>> biomart-server.bat
>> build.sh
>> fasta.sh
>> jetty.bat
>> Jetty-Service.exe
>> martconfigurator.bat
>> martrunner.bat
>> prunmgr.exe
>> runSoakTest.sh
>> biomart-server.sh
>> fasta.bat
>> generate-password.sh
>> jetty-service.conf
>> launch.sh
>> martconfigurator.sh
>> martrunner.sh
>> prunsrv.exe
>> test.sh
>>
>> Also, can you please point me to the documentation is located? I'm
> kinda
>> running blind.
>>
>> Thanks,
>> Heather
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 3:47 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> Heather,
>>
>> try:
>>      ant clean
>> and then
>>      ant
>>
>> also, please make sure you are running the above commands from the
>> following directory:
>>
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>
>> thanks
>> Syed
>>
>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>> Hi,
>>>
>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>> fixes the copy/paste URL bug. I ran
>>>
>>> svn update
>>>
>>> ant
>>>
>>> When I ran ant, I received the following compiler error:
>>>
>>> Buildfile: build.xml
>>>
>>> -load.properties:
>>>
>>> -init:
>>>
>>> compile.main:
>>>
>>>        [javac] Compiling 114 source files to
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>
>>>        [javac] ----------
>>>
>>>        [javac] 1. ERROR in
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/

>> utils/McGuiUtils.java (at line 1)
>>>
>>>        [javac]     package org.biomart.configurator.utils;
>>>
>>>        [javac]     ^^
>>>
>>>        [javac] The type Enum is not generic; it cannot be
> parameterized
>> with arguments<McGuiUtils>
>>>
>>>        [javac] ----------
>>>
>>>        [javac] 1 problem (1 error)
>>>
>>> BUILD FAILED
>>>
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>> failed; see the compiler error output for details.
>>>
>>> This is the portion of the McGuiType.java script that is having
> issues
>>>
>>> ...
>>>
>>> /**
>>>
>>>     * this class should not be used for web, should only be used for
>>>
>>>     * MartConfigurator GUI.
>>>
>>>     */
>>>
>>> public enum McGuiUtils {
>>>
>>>            INSTANCE;
>>>
>>>            private McGuiType guiType;
>>>
>>> ...
>>>
>>> What am I missing?
>>>
>>> Thanks,
>>>
>>> Heather
>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
let me have the output of these:

java -version
javac -version
ant -version


On 10/02/2011 00:15, Estrella, Heather wrote:

> I just get the Enum error. I just tried re-downloading a clean version
> of rc4 to see if I can get that to run a little more smoothly. The
> install that we had is pretty much messed up until the java compilation
> error is resolved.
>
> Here's the exact sequence of commands I've run:
>
> svn update
> ant clean
> ant
>
> I've tried re-running them in that sequence and here's the output:
>
> -bash-3.2$ svn update
> At revision 7145.
>
> -bash-3.2$ ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>   [delete] Deleting directory
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>   [delete] Deleting directory
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>
> BUILD SUCCESSFUL
>
> -bash-3.2$ ant
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>
> compile.main:
>    [javac] Compiling 455 source files to
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>    [javac] ----------
>    [javac] 1. ERROR in
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope
> ration.java (at line 1)
>    [javac]     package org.biomart.api.enums;
>    [javac]     ^^
>    [javac] The type Enum is not generic; it cannot be
> parameterized with arguments<Operation>
> [javac] ----------
>
>    [javac] 1 problem (1 error)
>
> BUILD FAILED
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
> failed; see the compiler error output for details.
>
> Total time: 1 second
>
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:16 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
> run ant
>
> You need to run:
>
> ant
>
> after ant clean.
>
> then it will recreate the dist/
>
> and then run:
>
> ./dist/scripts/biomart-server.sh start
>
>
>
>
> On 10/02/2011 00:07, Estrella, Heather wrote:
>> Thanks Syed,
>>
>> When I ran the 'ant clean' the first time, it deleted the dist
> directory
>> and the only place I could find the biomart-server.sh script is now in
>> the scripts directory located at $BIOMART_HOME
>>
>> bash-3.2$ ant clean
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> clean:
>>
>> BUILD SUCCESSFUL
>> Total time: 0 seconds
>>
>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
> really
>> changed the directory structure from what I was previously used to
> (i.e.
>> dist/scripts, etc.). because there is now a "plugins" directory is why
> I
>> thought maybe "svn update" updated my original rc3 installation to
> rc4.
>> However, even in the rc4 install that we have, there is still the dist
>> directory so I don't know what's going on.
>> ant.properties
>> build_test.xml
>> build.xml
>> conf
>> ext
>> images
>> lib
>> plugins
>> registry
>> scripts
>> src
>> start
>> test
>> testdata
>> voldemort
>> web
>>
>>
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:08 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> Heather,
>>
>> 1- please send me the console output when you run 'ant'
>>
>> 2- to start/stop biomart server, the commands are:
>>
>> ./dist/scripts/biomart-server.sh stop
>> ./dist/scripts/biomart-server.sh start
>>
>> thats from the dist directory. let me know if that helps.
>>
>> Syed
>>
>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>> Thanks Syed,
>>>
>>> That got me past the ant problem. However, it looks like running svn
>>> update automatically took my rc3 code to rc4.
>>>
>>> I'm trying to start my biomart server back up using "
>>> ./scripts/biomart-server.sh start" and I get the following error:
>>> ** ERROR:
>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>> readable!
>>>
>>> This jar file doesn't exist in the scripts directory. It isn't found
>>> anywhere in the installation path.
>>>
>>> Here is a list of what is in the scripts directory:
>>> biomart-server.bat
>>> build.sh
>>> fasta.sh
>>> jetty.bat
>>> Jetty-Service.exe
>>> martconfigurator.bat
>>> martrunner.bat
>>> prunmgr.exe
>>> runSoakTest.sh
>>> biomart-server.sh
>>> fasta.bat
>>> generate-password.sh
>>> jetty-service.conf
>>> launch.sh
>>> martconfigurator.sh
>>> martrunner.sh
>>> prunsrv.exe
>>> test.sh
>>>
>>> Also, can you please point me to the documentation is located? I'm
>> kinda
>>> running blind.
>>>
>>> Thanks,
>>> Heather
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> Heather,
>>>
>>> try:
>>>       ant clean
>>> and then
>>>       ant
>>>
>>> also, please make sure you are running the above commands from the
>>> following directory:
>>>
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>
>>> thanks
>>> Syed
>>>
>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>> Hi,
>>>>
>>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>>> fixes the copy/paste URL bug. I ran
>>>>
>>>> svn update
>>>>
>>>> ant
>>>>
>>>> When I ran ant, I received the following compiler error:
>>>>
>>>> Buildfile: build.xml
>>>>
>>>> -load.properties:
>>>>
>>>> -init:
>>>>
>>>> compile.main:
>>>>
>>>>         [javac] Compiling 114 source files to
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>
>>>>         [javac] ----------
>>>>
>>>>         [javac] 1. ERROR in
>>>
>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
>>> utils/McGuiUtils.java (at line 1)
>>>>
>>>>         [javac]     package org.biomart.configurator.utils;
>>>>
>>>>         [javac]     ^^
>>>>
>>>>         [javac] The type Enum is not generic; it cannot be
>> parameterized
>>> with arguments<McGuiUtils>
>>>>
>>>>         [javac] ----------
>>>>
>>>>         [javac] 1 problem (1 error)
>>>>
>>>> BUILD FAILED
>>>>
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>> failed; see the compiler error output for details.
>>>>
>>>> This is the portion of the McGuiType.java script that is having
>> issues
>>>>
>>>> ...
>>>>
>>>> /**
>>>>
>>>>      * this class should not be used for web, should only be used for
>>>>
>>>>      * MartConfigurator GUI.
>>>>
>>>>      */
>>>>
>>>> public enum McGuiUtils {
>>>>
>>>>             INSTANCE;
>>>>
>>>>             private McGuiType guiType;
>>>>
>>>> ...
>>>>
>>>> What am I missing?
>>>>
>>>> Thanks,
>>>>
>>>> Heather
>>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
I was just thinking the same thing because I got the same error with the
newly downloaded code.

-bash-3.2$ java -version
java version "1.6.0_05"
Java(TM) SE Runtime Environment (build 1.6.0_05-b13)
Java HotSpot(TM) 64-Bit Server VM (build 10.0-b19, mixed mode)

-bash-3.2$ javac -version
Eclipse Java Compiler v_677_R32x, 3.2.1 release, Copyright IBM Corp
2000, 2006. All rights reserved.

-bash-3.2$ ant -version
Apache Ant version 1.6.5 compiled on January 6 2007

-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 4:25 PM
To: Estrella, Heather
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

let me have the output of these:

java -version
javac -version
ant -version


On 10/02/2011 00:15, Estrella, Heather wrote:
> I just get the Enum error. I just tried re-downloading a clean version
> of rc4 to see if I can get that to run a little more smoothly. The
> install that we had is pretty much messed up until the java
compilation

> error is resolved.
>
> Here's the exact sequence of commands I've run:
>
> svn update
> ant clean
> ant
>
> I've tried re-running them in that sequence and here's the output:
>
> -bash-3.2$ svn update
> At revision 7145.
>
> -bash-3.2$ ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>   [delete] Deleting directory
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>   [delete] Deleting directory
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>
> BUILD SUCCESSFUL
>
> -bash-3.2$ ant
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>
> compile.main:
>    [javac] Compiling 455 source files to
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>    [javac] ----------
>    [javac] 1. ERROR in
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope

> ration.java (at line 1)
>    [javac]     package org.biomart.api.enums;
>    [javac]     ^^
>    [javac] The type Enum is not generic; it cannot be
> parameterized with arguments<Operation>
> [javac] ----------
>
>    [javac] 1 problem (1 error)
>
> BUILD FAILED
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
> failed; see the compiler error output for details.
>
> Total time: 1 second
>
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:16 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
when

> run ant
>
> You need to run:
>
> ant
>
> after ant clean.
>
> then it will recreate the dist/
>
> and then run:
>
> ./dist/scripts/biomart-server.sh start
>
>
>
>
> On 10/02/2011 00:07, Estrella, Heather wrote:
>> Thanks Syed,
>>
>> When I ran the 'ant clean' the first time, it deleted the dist
> directory
>> and the only place I could find the biomart-server.sh script is now
in

>> the scripts directory located at $BIOMART_HOME
>>
>> bash-3.2$ ant clean
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> clean:
>>
>> BUILD SUCCESSFUL
>> Total time: 0 seconds
>>
>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
> really
>> changed the directory structure from what I was previously used to
> (i.e.
>> dist/scripts, etc.). because there is now a "plugins" directory is
why
> I
>> thought maybe "svn update" updated my original rc3 installation to
> rc4.
>> However, even in the rc4 install that we have, there is still the
dist

>> directory so I don't know what's going on.
>> ant.properties
>> build_test.xml
>> build.xml
>> conf
>> ext
>> images
>> lib
>> plugins
>> registry
>> scripts
>> src
>> start
>> test
>> testdata
>> voldemort
>> web
>>
>>
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:08 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> Heather,
>>
>> 1- please send me the console output when you run 'ant'
>>
>> 2- to start/stop biomart server, the commands are:
>>
>> ./dist/scripts/biomart-server.sh stop
>> ./dist/scripts/biomart-server.sh start
>>
>> thats from the dist directory. let me know if that helps.
>>
>> Syed
>>
>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>> Thanks Syed,
>>>
>>> That got me past the ant problem. However, it looks like running svn
>>> update automatically took my rc3 code to rc4.
>>>
>>> I'm trying to start my biomart server back up using "
>>> ./scripts/biomart-server.sh start" and I get the following error:
>>> ** ERROR:
>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>> readable!
>>>
>>> This jar file doesn't exist in the scripts directory. It isn't found
>>> anywhere in the installation path.
>>>
>>> Here is a list of what is in the scripts directory:
>>> biomart-server.bat
>>> build.sh
>>> fasta.sh
>>> jetty.bat
>>> Jetty-Service.exe
>>> martconfigurator.bat
>>> martrunner.bat
>>> prunmgr.exe
>>> runSoakTest.sh
>>> biomart-server.sh
>>> fasta.bat
>>> generate-password.sh
>>> jetty-service.conf
>>> launch.sh
>>> martconfigurator.sh
>>> martrunner.sh
>>> prunsrv.exe
>>> test.sh
>>>
>>> Also, can you please point me to the documentation is located? I'm
>> kinda
>>> running blind.
>>>
>>> Thanks,
>>> Heather
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> Heather,
>>>
>>> try:
>>>       ant clean
>>> and then
>>>       ant
>>>
>>> also, please make sure you are running the above commands from the
>>> following directory:
>>>
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>
>>> thanks
>>> Syed
>>>
>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>> Hi,
>>>>
>>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>>> fixes the copy/paste URL bug. I ran
>>>>
>>>> svn update
>>>>
>>>> ant
>>>>
>>>> When I ran ant, I received the following compiler error:
>>>>
>>>> Buildfile: build.xml
>>>>
>>>> -load.properties:
>>>>
>>>> -init:
>>>>
>>>> compile.main:
>>>>
>>>>         [javac] Compiling 114 source files to
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>
>>>>         [javac] ----------
>>>>
>>>>         [javac] 1. ERROR in
>>>
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/

>>> utils/McGuiUtils.java (at line 1)
>>>>
>>>>         [javac]     package org.biomart.configurator.utils;
>>>>
>>>>         [javac]     ^^
>>>>
>>>>         [javac] The type Enum is not generic; it cannot be
>> parameterized
>>> with arguments<McGuiUtils>
>>>>
>>>>         [javac] ----------
>>>>
>>>>         [javac] 1 problem (1 error)
>>>>
>>>> BUILD FAILED
>>>>
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>> failed; see the compiler error output for details.
>>>>
>>>> This is the portion of the McGuiType.java script that is having
>> issues
>>>>
>>>> ...
>>>>
>>>> /**
>>>>
>>>>      * this class should not be used for web, should only be used
for

>>>>
>>>>      * MartConfigurator GUI.
>>>>
>>>>      */
>>>>
>>>> public enum McGuiUtils {
>>>>
>>>>             INSTANCE;
>>>>
>>>>             private McGuiType guiType;
>>>>
>>>> ...
>>>>
>>>> What am I missing?
>>>>
>>>> Thanks,
>>>>
>>>> Heather
>>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when runant

Estrella, Heather
Hi Syed,

I've tried downloading and installing both rc3 and rc4 onto a completely
different system (all pre-reqs met) and get the same compilation error.

I'm not sure what else to try.

Heather

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Estrella, Heather
Sent: Wednesday, February 09, 2011 4:21 PM
To: Syed Haider
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
runant

I was just thinking the same thing because I got the same error with the
newly downloaded code.

-bash-3.2$ java -version
java version "1.6.0_05"
Java(TM) SE Runtime Environment (build 1.6.0_05-b13)
Java HotSpot(TM) 64-Bit Server VM (build 10.0-b19, mixed mode)

-bash-3.2$ javac -version
Eclipse Java Compiler v_677_R32x, 3.2.1 release, Copyright IBM Corp
2000, 2006. All rights reserved.

-bash-3.2$ ant -version
Apache Ant version 1.6.5 compiled on January 6 2007

-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 4:25 PM
To: Estrella, Heather
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

let me have the output of these:

java -version
javac -version
ant -version


On 10/02/2011 00:15, Estrella, Heather wrote:
> I just get the Enum error. I just tried re-downloading a clean version
> of rc4 to see if I can get that to run a little more smoothly. The
> install that we had is pretty much messed up until the java
compilation

> error is resolved.
>
> Here's the exact sequence of commands I've run:
>
> svn update
> ant clean
> ant
>
> I've tried re-running them in that sequence and here's the output:
>
> -bash-3.2$ svn update
> At revision 7145.
>
> -bash-3.2$ ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>   [delete] Deleting directory
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>   [delete] Deleting directory
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>
> BUILD SUCCESSFUL
>
> -bash-3.2$ ant
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>    [mkdir] Created dir:
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>
> compile.main:
>    [javac] Compiling 455 source files to
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>    [javac] ----------
>    [javac] 1. ERROR in
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope

> ration.java (at line 1)
>    [javac]     package org.biomart.api.enums;
>    [javac]     ^^
>    [javac] The type Enum is not generic; it cannot be
> parameterized with arguments<Operation>
> [javac] ----------
>
>    [javac] 1 problem (1 error)
>
> BUILD FAILED
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
> failed; see the compiler error output for details.
>
> Total time: 1 second
>
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:16 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
when

> run ant
>
> You need to run:
>
> ant
>
> after ant clean.
>
> then it will recreate the dist/
>
> and then run:
>
> ./dist/scripts/biomart-server.sh start
>
>
>
>
> On 10/02/2011 00:07, Estrella, Heather wrote:
>> Thanks Syed,
>>
>> When I ran the 'ant clean' the first time, it deleted the dist
> directory
>> and the only place I could find the biomart-server.sh script is now
in

>> the scripts directory located at $BIOMART_HOME
>>
>> bash-3.2$ ant clean
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> clean:
>>
>> BUILD SUCCESSFUL
>> Total time: 0 seconds
>>
>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
> really
>> changed the directory structure from what I was previously used to
> (i.e.
>> dist/scripts, etc.). because there is now a "plugins" directory is
why
> I
>> thought maybe "svn update" updated my original rc3 installation to
> rc4.
>> However, even in the rc4 install that we have, there is still the
dist

>> directory so I don't know what's going on.
>> ant.properties
>> build_test.xml
>> build.xml
>> conf
>> ext
>> images
>> lib
>> plugins
>> registry
>> scripts
>> src
>> start
>> test
>> testdata
>> voldemort
>> web
>>
>>
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:08 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> Heather,
>>
>> 1- please send me the console output when you run 'ant'
>>
>> 2- to start/stop biomart server, the commands are:
>>
>> ./dist/scripts/biomart-server.sh stop
>> ./dist/scripts/biomart-server.sh start
>>
>> thats from the dist directory. let me know if that helps.
>>
>> Syed
>>
>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>> Thanks Syed,
>>>
>>> That got me past the ant problem. However, it looks like running svn
>>> update automatically took my rc3 code to rc4.
>>>
>>> I'm trying to start my biomart server back up using "
>>> ./scripts/biomart-server.sh start" and I get the following error:
>>> ** ERROR:
>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>> readable!
>>>
>>> This jar file doesn't exist in the scripts directory. It isn't found
>>> anywhere in the installation path.
>>>
>>> Here is a list of what is in the scripts directory:
>>> biomart-server.bat
>>> build.sh
>>> fasta.sh
>>> jetty.bat
>>> Jetty-Service.exe
>>> martconfigurator.bat
>>> martrunner.bat
>>> prunmgr.exe
>>> runSoakTest.sh
>>> biomart-server.sh
>>> fasta.bat
>>> generate-password.sh
>>> jetty-service.conf
>>> launch.sh
>>> martconfigurator.sh
>>> martrunner.sh
>>> prunsrv.exe
>>> test.sh
>>>
>>> Also, can you please point me to the documentation is located? I'm
>> kinda
>>> running blind.
>>>
>>> Thanks,
>>> Heather
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> Heather,
>>>
>>> try:
>>>       ant clean
>>> and then
>>>       ant
>>>
>>> also, please make sure you are running the above commands from the
>>> following directory:
>>>
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>
>>> thanks
>>> Syed
>>>
>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>> Hi,
>>>>
>>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>>> fixes the copy/paste URL bug. I ran
>>>>
>>>> svn update
>>>>
>>>> ant
>>>>
>>>> When I ran ant, I received the following compiler error:
>>>>
>>>> Buildfile: build.xml
>>>>
>>>> -load.properties:
>>>>
>>>> -init:
>>>>
>>>> compile.main:
>>>>
>>>>         [javac] Compiling 114 source files to
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>
>>>>         [javac] ----------
>>>>
>>>>         [javac] 1. ERROR in
>>>
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/

>>> utils/McGuiUtils.java (at line 1)
>>>>
>>>>         [javac]     package org.biomart.configurator.utils;
>>>>
>>>>         [javac]     ^^
>>>>
>>>>         [javac] The type Enum is not generic; it cannot be
>> parameterized
>>> with arguments<McGuiUtils>
>>>>
>>>>         [javac] ----------
>>>>
>>>>         [javac] 1 problem (1 error)
>>>>
>>>> BUILD FAILED
>>>>
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>> failed; see the compiler error output for details.
>>>>
>>>> This is the portion of the McGuiType.java script that is having
>> issues
>>>>
>>>> ...
>>>>
>>>> /**
>>>>
>>>>      * this class should not be used for web, should only be used
for

>>>>
>>>>      * MartConfigurator GUI.
>>>>
>>>>      */
>>>>
>>>> public enum McGuiUtils {
>>>>
>>>>             INSTANCE;
>>>>
>>>>             private McGuiType guiType;
>>>>
>>>> ...
>>>>
>>>> What am I missing?
>>>>
>>>> Thanks,
>>>>
>>>> Heather
>>>>
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
In reply to this post by Estrella, Heather
Right, my suspicion is the java compile (javac). It seems to be an old
java. By any chance, do you a non-eclipse version of javac and that is
javac 1.6?



On 10/02/2011 00:20, Estrella, Heather wrote:

> I was just thinking the same thing because I got the same error with the
> newly downloaded code.
>
> -bash-3.2$ java -version
> java version "1.6.0_05"
> Java(TM) SE Runtime Environment (build 1.6.0_05-b13)
> Java HotSpot(TM) 64-Bit Server VM (build 10.0-b19, mixed mode)
>
> -bash-3.2$ javac -version
> Eclipse Java Compiler v_677_R32x, 3.2.1 release, Copyright IBM Corp
> 2000, 2006. All rights reserved.
>
> -bash-3.2$ ant -version
> Apache Ant version 1.6.5 compiled on January 6 2007
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:25 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
> run ant
>
> let me have the output of these:
>
> java -version
> javac -version
> ant -version
>
>
> On 10/02/2011 00:15, Estrella, Heather wrote:
>> I just get the Enum error. I just tried re-downloading a clean version
>> of rc4 to see if I can get that to run a little more smoothly. The
>> install that we had is pretty much messed up until the java
> compilation
>> error is resolved.
>>
>> Here's the exact sequence of commands I've run:
>>
>> svn update
>> ant clean
>> ant
>>
>> I've tried re-running them in that sequence and here's the output:
>>
>> -bash-3.2$ svn update
>> At revision 7145.
>>
>> -bash-3.2$ ant clean
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> clean:
>>   [delete] Deleting directory
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>>   [delete] Deleting directory
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>>
>> BUILD SUCCESSFUL
>>
>> -bash-3.2$ ant
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> -init:
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>>
>> compile.main:
>>    [javac] Compiling 455 source files to
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>    [javac] ----------
>>    [javac] 1. ERROR in
>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope
>> ration.java (at line 1)
>>    [javac]     package org.biomart.api.enums;
>>    [javac]     ^^
>>    [javac] The type Enum is not generic; it cannot be
>> parameterized with arguments<Operation>
>> [javac] ----------
>>
>>    [javac] 1 problem (1 error)
>>
>> BUILD FAILED
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>> failed; see the compiler error output for details.
>>
>> Total time: 1 second
>>
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:16 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> You need to run:
>>
>> ant
>>
>> after ant clean.
>>
>> then it will recreate the dist/
>>
>> and then run:
>>
>> ./dist/scripts/biomart-server.sh start
>>
>>
>>
>>
>> On 10/02/2011 00:07, Estrella, Heather wrote:
>>> Thanks Syed,
>>>
>>> When I ran the 'ant clean' the first time, it deleted the dist
>> directory
>>> and the only place I could find the biomart-server.sh script is now
> in
>>> the scripts directory located at $BIOMART_HOME
>>>
>>> bash-3.2$ ant clean
>>> Buildfile: build.xml
>>>
>>> -load.properties:
>>>
>>> clean:
>>>
>>> BUILD SUCCESSFUL
>>> Total time: 0 seconds
>>>
>>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
>> really
>>> changed the directory structure from what I was previously used to
>> (i.e.
>>> dist/scripts, etc.). because there is now a "plugins" directory is
> why
>> I
>>> thought maybe "svn update" updated my original rc3 installation to
>> rc4.
>>> However, even in the rc4 install that we have, there is still the
> dist
>>> directory so I don't know what's going on.
>>> ant.properties
>>> build_test.xml
>>> build.xml
>>> conf
>>> ext
>>> images
>>> lib
>>> plugins
>>> registry
>>> scripts
>>> src
>>> start
>>> test
>>> testdata
>>> voldemort
>>> web
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 4:08 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> Heather,
>>>
>>> 1- please send me the console output when you run 'ant'
>>>
>>> 2- to start/stop biomart server, the commands are:
>>>
>>> ./dist/scripts/biomart-server.sh stop
>>> ./dist/scripts/biomart-server.sh start
>>>
>>> thats from the dist directory. let me know if that helps.
>>>
>>> Syed
>>>
>>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>>> Thanks Syed,
>>>>
>>>> That got me past the ant problem. However, it looks like running svn
>>>> update automatically took my rc3 code to rc4.
>>>>
>>>> I'm trying to start my biomart server back up using "
>>>> ./scripts/biomart-server.sh start" and I get the following error:
>>>> ** ERROR:
>>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>>> readable!
>>>>
>>>> This jar file doesn't exist in the scripts directory. It isn't found
>>>> anywhere in the installation path.
>>>>
>>>> Here is a list of what is in the scripts directory:
>>>> biomart-server.bat
>>>> build.sh
>>>> fasta.sh
>>>> jetty.bat
>>>> Jetty-Service.exe
>>>> martconfigurator.bat
>>>> martrunner.bat
>>>> prunmgr.exe
>>>> runSoakTest.sh
>>>> biomart-server.sh
>>>> fasta.bat
>>>> generate-password.sh
>>>> jetty-service.conf
>>>> launch.sh
>>>> martconfigurator.sh
>>>> martrunner.sh
>>>> prunsrv.exe
>>>> test.sh
>>>>
>>>> Also, can you please point me to the documentation is located? I'm
>>> kinda
>>>> running blind.
>>>>
>>>> Thanks,
>>>> Heather
>>>>
>>>> -----Original Message-----
>>>> From: Syed Haider [mailto:[hidden email]]
>>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>>> To: Estrella, Heather
>>>> Cc: [hidden email]
>>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>>> when
>>>> run ant
>>>>
>>>> Heather,
>>>>
>>>> try:
>>>>        ant clean
>>>> and then
>>>>        ant
>>>>
>>>> also, please make sure you are running the above commands from the
>>>> following directory:
>>>>
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>>
>>>> thanks
>>>> Syed
>>>>
>>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>>> Hi,
>>>>>
>>>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>>>> fixes the copy/paste URL bug. I ran
>>>>>
>>>>> svn update
>>>>>
>>>>> ant
>>>>>
>>>>> When I ran ant, I received the following compiler error:
>>>>>
>>>>> Buildfile: build.xml
>>>>>
>>>>> -load.properties:
>>>>>
>>>>> -init:
>>>>>
>>>>> compile.main:
>>>>>
>>>>>          [javac] Compiling 114 source files to
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>>
>>>>>          [javac] ----------
>>>>>
>>>>>          [javac] 1. ERROR in
>>>>
>>>
>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
>>>> utils/McGuiUtils.java (at line 1)
>>>>>
>>>>>          [javac]     package org.biomart.configurator.utils;
>>>>>
>>>>>          [javac]     ^^
>>>>>
>>>>>          [javac] The type Enum is not generic; it cannot be
>>> parameterized
>>>> with arguments<McGuiUtils>
>>>>>
>>>>>          [javac] ----------
>>>>>
>>>>>          [javac] 1 problem (1 error)
>>>>>
>>>>> BUILD FAILED
>>>>>
>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>>> failed; see the compiler error output for details.
>>>>>
>>>>> This is the portion of the McGuiType.java script that is having
>>> issues
>>>>>
>>>>> ...
>>>>>
>>>>> /**
>>>>>
>>>>>       * this class should not be used for web, should only be used
> for
>>>>>
>>>>>       * MartConfigurator GUI.
>>>>>
>>>>>       */
>>>>>
>>>>> public enum McGuiUtils {
>>>>>
>>>>>              INSTANCE;
>>>>>
>>>>>              private McGuiType guiType;
>>>>>
>>>>> ...
>>>>>
>>>>> What am I missing?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Heather
>>>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
Hi Syed,

I tried both javac 1.6.0_05 and 1.6.0_21 and both give me the same
error.

% javac -version
        javac 1.6.0_05


% ant clean
Buildfile: build.xml

-load.properties:

clean:
   [delete] Deleting directory /lscratch/apps/BioMart8/test_he/dist
   [delete] Deleting directory /lscratch/apps/BioMart8/test_he/build

BUILD SUCCESSFUL
Total time: 0 seconds



% ant
Buildfile: build.xml

-load.properties:

-init:
    [mkdir] Created dir:
/lscratch/apps/BioMart8/test_he/build/classes/main/META-INF
    [mkdir] Created dir:
/lscratch/apps/BioMart8/test_he/build/classes/start
    [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/build/lib
    [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/dist/web/work
    [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/dist/logs
    [mkdir] Created dir:
/lscratch/apps/BioMart8/test_he/dist/registry/linkindices

compile.main:
    [javac] Compiling 451 source files to
/lscratch/apps/BioMart8/test_he/build/classes/main
    [javac] ----------
    [javac] 1. ERROR in
/lscratch/apps/BioMart8/test_he/src/org/biomart/api/enums/BiomartVersion
.java (at line 1)
    [javac]     package org.biomart.api.enums;
    [javac]     ^^
    [javac] The type Enum is not generic; it cannot be parameterized
with arguments <BiomartVersion>
    [javac] ----------
    [javac] 1 problem (1 error)

BUILD FAILED
/lscratch/apps/BioMart8/test_he/build.xml:24: Compile failed; see the
compiler error output for details.

-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 4:44 PM
To: Estrella, Heather
Cc: [hidden email]
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

Right, my suspicion is the java compile (javac). It seems to be an old
java. By any chance, do you a non-eclipse version of javac and that is
javac 1.6?



On 10/02/2011 00:20, Estrella, Heather wrote:
> I was just thinking the same thing because I got the same error with
the

> newly downloaded code.
>
> -bash-3.2$ java -version
> java version "1.6.0_05"
> Java(TM) SE Runtime Environment (build 1.6.0_05-b13)
> Java HotSpot(TM) 64-Bit Server VM (build 10.0-b19, mixed mode)
>
> -bash-3.2$ javac -version
> Eclipse Java Compiler v_677_R32x, 3.2.1 release, Copyright IBM Corp
> 2000, 2006. All rights reserved.
>
> -bash-3.2$ ant -version
> Apache Ant version 1.6.5 compiled on January 6 2007
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:25 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
when

> run ant
>
> let me have the output of these:
>
> java -version
> javac -version
> ant -version
>
>
> On 10/02/2011 00:15, Estrella, Heather wrote:
>> I just get the Enum error. I just tried re-downloading a clean
version

>> of rc4 to see if I can get that to run a little more smoothly. The
>> install that we had is pretty much messed up until the java
> compilation
>> error is resolved.
>>
>> Here's the exact sequence of commands I've run:
>>
>> svn update
>> ant clean
>> ant
>>
>> I've tried re-running them in that sequence and here's the output:
>>
>> -bash-3.2$ svn update
>> At revision 7145.
>>
>> -bash-3.2$ ant clean
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> clean:
>>   [delete] Deleting directory
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>>   [delete] Deleting directory
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>>
>> BUILD SUCCESSFUL
>>
>> -bash-3.2$ ant
>> Buildfile: build.xml
>>
>> -load.properties:
>>
>> -init:
>>    [mkdir] Created dir:
>>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF

>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>>    [mkdir] Created dir:
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>>
>> compile.main:
>>    [javac] Compiling 455 source files to
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>    [javac] ----------
>>    [javac] 1. ERROR in
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope

>> ration.java (at line 1)
>>    [javac]     package org.biomart.api.enums;
>>    [javac]     ^^
>>    [javac] The type Enum is not generic; it cannot be
>> parameterized with arguments<Operation>
>> [javac] ----------
>>
>>    [javac] 1 problem (1 error)
>>
>> BUILD FAILED
>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>> failed; see the compiler error output for details.
>>
>> Total time: 1 second
>>
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:16 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> You need to run:
>>
>> ant
>>
>> after ant clean.
>>
>> then it will recreate the dist/
>>
>> and then run:
>>
>> ./dist/scripts/biomart-server.sh start
>>
>>
>>
>>
>> On 10/02/2011 00:07, Estrella, Heather wrote:
>>> Thanks Syed,
>>>
>>> When I ran the 'ant clean' the first time, it deleted the dist
>> directory
>>> and the only place I could find the biomart-server.sh script is now
> in
>>> the scripts directory located at $BIOMART_HOME
>>>
>>> bash-3.2$ ant clean
>>> Buildfile: build.xml
>>>
>>> -load.properties:
>>>
>>> clean:
>>>
>>> BUILD SUCCESSFUL
>>> Total time: 0 seconds
>>>
>>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
>> really
>>> changed the directory structure from what I was previously used to
>> (i.e.
>>> dist/scripts, etc.). because there is now a "plugins" directory is
> why
>> I
>>> thought maybe "svn update" updated my original rc3 installation to
>> rc4.
>>> However, even in the rc4 install that we have, there is still the
> dist
>>> directory so I don't know what's going on.
>>> ant.properties
>>> build_test.xml
>>> build.xml
>>> conf
>>> ext
>>> images
>>> lib
>>> plugins
>>> registry
>>> scripts
>>> src
>>> start
>>> test
>>> testdata
>>> voldemort
>>> web
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 4:08 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> Heather,
>>>
>>> 1- please send me the console output when you run 'ant'
>>>
>>> 2- to start/stop biomart server, the commands are:
>>>
>>> ./dist/scripts/biomart-server.sh stop
>>> ./dist/scripts/biomart-server.sh start
>>>
>>> thats from the dist directory. let me know if that helps.
>>>
>>> Syed
>>>
>>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>>> Thanks Syed,
>>>>
>>>> That got me past the ant problem. However, it looks like running
svn
>>>> update automatically took my rc3 code to rc4.
>>>>
>>>> I'm trying to start my biomart server back up using "
>>>> ./scripts/biomart-server.sh start" and I get the following error:
>>>> ** ERROR:
>>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>>> readable!
>>>>
>>>> This jar file doesn't exist in the scripts directory. It isn't
found

>>>> anywhere in the installation path.
>>>>
>>>> Here is a list of what is in the scripts directory:
>>>> biomart-server.bat
>>>> build.sh
>>>> fasta.sh
>>>> jetty.bat
>>>> Jetty-Service.exe
>>>> martconfigurator.bat
>>>> martrunner.bat
>>>> prunmgr.exe
>>>> runSoakTest.sh
>>>> biomart-server.sh
>>>> fasta.bat
>>>> generate-password.sh
>>>> jetty-service.conf
>>>> launch.sh
>>>> martconfigurator.sh
>>>> martrunner.sh
>>>> prunsrv.exe
>>>> test.sh
>>>>
>>>> Also, can you please point me to the documentation is located? I'm
>>> kinda
>>>> running blind.
>>>>
>>>> Thanks,
>>>> Heather
>>>>
>>>> -----Original Message-----
>>>> From: Syed Haider [mailto:[hidden email]]
>>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>>> To: Estrella, Heather
>>>> Cc: [hidden email]
>>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>>> when
>>>> run ant
>>>>
>>>> Heather,
>>>>
>>>> try:
>>>>        ant clean
>>>> and then
>>>>        ant
>>>>
>>>> also, please make sure you are running the above commands from the
>>>> following directory:
>>>>
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>>
>>>> thanks
>>>> Syed
>>>>
>>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>>> Hi,
>>>>>
>>>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>>>> fixes the copy/paste URL bug. I ran
>>>>>
>>>>> svn update
>>>>>
>>>>> ant
>>>>>
>>>>> When I ran ant, I received the following compiler error:
>>>>>
>>>>> Buildfile: build.xml
>>>>>
>>>>> -load.properties:
>>>>>
>>>>> -init:
>>>>>
>>>>> compile.main:
>>>>>
>>>>>          [javac] Compiling 114 source files to
>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>>
>>>>>          [javac] ----------
>>>>>
>>>>>          [javac] 1. ERROR in
>>>>
>>>
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/

>>>> utils/McGuiUtils.java (at line 1)
>>>>>
>>>>>          [javac]     package org.biomart.configurator.utils;
>>>>>
>>>>>          [javac]     ^^
>>>>>
>>>>>          [javac] The type Enum is not generic; it cannot be
>>> parameterized
>>>> with arguments<McGuiUtils>
>>>>>
>>>>>          [javac] ----------
>>>>>
>>>>>          [javac] 1 problem (1 error)
>>>>>
>>>>> BUILD FAILED
>>>>>
>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>>> failed; see the compiler error output for details.
>>>>>
>>>>> This is the portion of the McGuiType.java script that is having
>>> issues
>>>>>
>>>>> ...
>>>>>
>>>>> /**
>>>>>
>>>>>       * this class should not be used for web, should only be used
> for
>>>>>
>>>>>       * MartConfigurator GUI.
>>>>>
>>>>>       */
>>>>>
>>>>> public enum McGuiUtils {
>>>>>
>>>>>              INSTANCE;
>>>>>
>>>>>              private McGuiType guiType;
>>>>>
>>>>> ...
>>>>>
>>>>> What am I missing?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Heather
>>>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Syed Haider
Ok, is ant using the same javac target. Usually ant uses the javac thats
in your JAVA_HOME

so please see where JAVA_HOME is pointing i-e

printenv JAVA_HOME

and then using that path, append:
/bin/javac -version
and see if thats the same as you sent in the last email ?





On 10/02/2011 01:13, Estrella, Heather wrote:

> Hi Syed,
>
> I tried both javac 1.6.0_05 and 1.6.0_21 and both give me the same
> error.
>
> % javac -version
>          javac 1.6.0_05
>
>
> % ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>     [delete] Deleting directory /lscratch/apps/BioMart8/test_he/dist
>     [delete] Deleting directory /lscratch/apps/BioMart8/test_he/build
>
> BUILD SUCCESSFUL
> Total time: 0 seconds
>
>
>
> % ant
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>      [mkdir] Created dir:
> /lscratch/apps/BioMart8/test_he/build/classes/main/META-INF
>      [mkdir] Created dir:
> /lscratch/apps/BioMart8/test_he/build/classes/start
>      [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/build/lib
>      [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/dist/web/work
>      [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/dist/logs
>      [mkdir] Created dir:
> /lscratch/apps/BioMart8/test_he/dist/registry/linkindices
>
> compile.main:
>      [javac] Compiling 451 source files to
> /lscratch/apps/BioMart8/test_he/build/classes/main
>      [javac] ----------
>      [javac] 1. ERROR in
> /lscratch/apps/BioMart8/test_he/src/org/biomart/api/enums/BiomartVersion
> .java (at line 1)
>      [javac]     package org.biomart.api.enums;
>      [javac]     ^^
>      [javac] The type Enum is not generic; it cannot be parameterized
> with arguments<BiomartVersion>
>      [javac] ----------
>      [javac] 1 problem (1 error)
>
> BUILD FAILED
> /lscratch/apps/BioMart8/test_he/build.xml:24: Compile failed; see the
> compiler error output for details.
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:44 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
> run ant
>
> Right, my suspicion is the java compile (javac). It seems to be an old
> java. By any chance, do you a non-eclipse version of javac and that is
> javac 1.6?
>
>
>
> On 10/02/2011 00:20, Estrella, Heather wrote:
>> I was just thinking the same thing because I got the same error with
> the
>> newly downloaded code.
>>
>> -bash-3.2$ java -version
>> java version "1.6.0_05"
>> Java(TM) SE Runtime Environment (build 1.6.0_05-b13)
>> Java HotSpot(TM) 64-Bit Server VM (build 10.0-b19, mixed mode)
>>
>> -bash-3.2$ javac -version
>> Eclipse Java Compiler v_677_R32x, 3.2.1 release, Copyright IBM Corp
>> 2000, 2006. All rights reserved.
>>
>> -bash-3.2$ ant -version
>> Apache Ant version 1.6.5 compiled on January 6 2007
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:25 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> let me have the output of these:
>>
>> java -version
>> javac -version
>> ant -version
>>
>>
>> On 10/02/2011 00:15, Estrella, Heather wrote:
>>> I just get the Enum error. I just tried re-downloading a clean
> version
>>> of rc4 to see if I can get that to run a little more smoothly. The
>>> install that we had is pretty much messed up until the java
>> compilation
>>> error is resolved.
>>>
>>> Here's the exact sequence of commands I've run:
>>>
>>> svn update
>>> ant clean
>>> ant
>>>
>>> I've tried re-running them in that sequence and here's the output:
>>>
>>> -bash-3.2$ svn update
>>>       At revision 7145.
>>>
>>> -bash-3.2$ ant clean
>>>       Buildfile: build.xml
>>>
>>>       -load.properties:
>>>
>>>       clean:
>>>          [delete] Deleting directory
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>>>          [delete] Deleting directory
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>>>
>>>       BUILD SUCCESSFUL
>>>
>>> -bash-3.2$ ant
>>>       Buildfile: build.xml
>>>
>>>       -load.properties:
>>>
>>>       -init:
>>>           [mkdir] Created dir:
>>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>>>
>>>       compile.main:
>>>           [javac] Compiling 455 source files to
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>           [javac] ----------
>>>           [javac] 1. ERROR in
>>>
>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope
>>> ration.java (at line 1)
>>>           [javac]     package org.biomart.api.enums;
>>>           [javac]     ^^
>>>           [javac] The type Enum is not generic; it cannot be
>>> parameterized with arguments<Operation>
>>>       [javac] ----------
>>>
>>>           [javac] 1 problem (1 error)
>>>
>>>       BUILD FAILED
>>>       /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>> failed; see the compiler error output for details.
>>>
>>>       Total time: 1 second
>>>
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 4:16 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> You need to run:
>>>
>>> ant
>>>
>>> after ant clean.
>>>
>>> then it will recreate the dist/
>>>
>>> and then run:
>>>
>>> ./dist/scripts/biomart-server.sh start
>>>
>>>
>>>
>>>
>>> On 10/02/2011 00:07, Estrella, Heather wrote:
>>>> Thanks Syed,
>>>>
>>>> When I ran the 'ant clean' the first time, it deleted the dist
>>> directory
>>>> and the only place I could find the biomart-server.sh script is now
>> in
>>>> the scripts directory located at $BIOMART_HOME
>>>>
>>>> bash-3.2$ ant clean
>>>> Buildfile: build.xml
>>>>
>>>> -load.properties:
>>>>
>>>> clean:
>>>>
>>>> BUILD SUCCESSFUL
>>>> Total time: 0 seconds
>>>>
>>>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
>>> really
>>>> changed the directory structure from what I was previously used to
>>> (i.e.
>>>> dist/scripts, etc.). because there is now a "plugins" directory is
>> why
>>> I
>>>> thought maybe "svn update" updated my original rc3 installation to
>>> rc4.
>>>> However, even in the rc4 install that we have, there is still the
>> dist
>>>> directory so I don't know what's going on.
>>>> ant.properties
>>>> build_test.xml
>>>> build.xml
>>>> conf
>>>> ext
>>>> images
>>>> lib
>>>> plugins
>>>> registry
>>>> scripts
>>>> src
>>>> start
>>>> test
>>>> testdata
>>>> voldemort
>>>> web
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Syed Haider [mailto:[hidden email]]
>>>> Sent: Wednesday, February 09, 2011 4:08 PM
>>>> To: Estrella, Heather
>>>> Cc: [hidden email]
>>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>>> when
>>>> run ant
>>>>
>>>> Heather,
>>>>
>>>> 1- please send me the console output when you run 'ant'
>>>>
>>>> 2- to start/stop biomart server, the commands are:
>>>>
>>>> ./dist/scripts/biomart-server.sh stop
>>>> ./dist/scripts/biomart-server.sh start
>>>>
>>>> thats from the dist directory. let me know if that helps.
>>>>
>>>> Syed
>>>>
>>>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>>>> Thanks Syed,
>>>>>
>>>>> That got me past the ant problem. However, it looks like running
> svn
>>>>> update automatically took my rc3 code to rc4.
>>>>>
>>>>> I'm trying to start my biomart server back up using "
>>>>> ./scripts/biomart-server.sh start" and I get the following error:
>>>>>     ** ERROR:
>>>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>>>> readable!
>>>>>
>>>>> This jar file doesn't exist in the scripts directory. It isn't
> found
>>>>> anywhere in the installation path.
>>>>>
>>>>> Here is a list of what is in the scripts directory:
>>>>> biomart-server.bat
>>>>> build.sh
>>>>> fasta.sh
>>>>> jetty.bat
>>>>> Jetty-Service.exe
>>>>> martconfigurator.bat
>>>>> martrunner.bat
>>>>> prunmgr.exe
>>>>> runSoakTest.sh
>>>>> biomart-server.sh
>>>>> fasta.bat
>>>>> generate-password.sh
>>>>> jetty-service.conf
>>>>> launch.sh
>>>>> martconfigurator.sh
>>>>> martrunner.sh
>>>>> prunsrv.exe
>>>>> test.sh
>>>>>
>>>>> Also, can you please point me to the documentation is located? I'm
>>>> kinda
>>>>> running blind.
>>>>>
>>>>> Thanks,
>>>>> Heather
>>>>>
>>>>> -----Original Message-----
>>>>> From: Syed Haider [mailto:[hidden email]]
>>>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>>>> To: Estrella, Heather
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>>>> when
>>>>> run ant
>>>>>
>>>>> Heather,
>>>>>
>>>>> try:
>>>>>         ant clean
>>>>> and then
>>>>>         ant
>>>>>
>>>>> also, please make sure you are running the above commands from the
>>>>> following directory:
>>>>>
>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>>>
>>>>> thanks
>>>>> Syed
>>>>>
>>>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to upgrade my RC3 installation to the new RC3 code that
>>>>> fixes the copy/paste URL bug. I ran
>>>>>>
>>>>>> svn update
>>>>>>
>>>>>> ant
>>>>>>
>>>>>> When I ran ant, I received the following compiler error:
>>>>>>
>>>>>> Buildfile: build.xml
>>>>>>
>>>>>> -load.properties:
>>>>>>
>>>>>> -init:
>>>>>>
>>>>>> compile.main:
>>>>>>
>>>>>>           [javac] Compiling 114 source files to
>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>>>
>>>>>>           [javac] ----------
>>>>>>
>>>>>>           [javac] 1. ERROR in
>>>>>
>>>>
>>>
>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/
>>>>> utils/McGuiUtils.java (at line 1)
>>>>>>
>>>>>>           [javac]     package org.biomart.configurator.utils;
>>>>>>
>>>>>>           [javac]     ^^
>>>>>>
>>>>>>           [javac] The type Enum is not generic; it cannot be
>>>> parameterized
>>>>> with arguments<McGuiUtils>
>>>>>>
>>>>>>           [javac] ----------
>>>>>>
>>>>>>           [javac] 1 problem (1 error)
>>>>>>
>>>>>> BUILD FAILED
>>>>>>
>>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>>>> failed; see the compiler error output for details.
>>>>>>
>>>>>> This is the portion of the McGuiType.java script that is having
>>>> issues
>>>>>>
>>>>>> ...
>>>>>>
>>>>>> /**
>>>>>>
>>>>>>        * this class should not be used for web, should only be used
>> for
>>>>>>
>>>>>>        * MartConfigurator GUI.
>>>>>>
>>>>>>        */
>>>>>>
>>>>>> public enum McGuiUtils {
>>>>>>
>>>>>>               INSTANCE;
>>>>>>
>>>>>>               private McGuiType guiType;
>>>>>>
>>>>>> ...
>>>>>>
>>>>>> What am I missing?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Heather
>>>>>>
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Re: [BioMart Users] svn update for rc3 get compiler error when run ant

Estrella, Heather
Alright, I think we got it. It was a mixture of java environment
settings and the java versions being used.

Thank you so much for your help and patience!
Heather

-----Original Message-----
From: Syed Haider [mailto:[hidden email]]
Sent: Wednesday, February 09, 2011 5:26 PM
To: Estrella, Heather
Cc: [hidden email]; Liu, Yu
Subject: Re: [BioMart Users] svn update for rc3 get compiler error when
run ant

Ok, is ant using the same javac target. Usually ant uses the javac thats

in your JAVA_HOME

so please see where JAVA_HOME is pointing i-e

printenv JAVA_HOME

and then using that path, append:
/bin/javac -version
and see if thats the same as you sent in the last email ?





On 10/02/2011 01:13, Estrella, Heather wrote:

> Hi Syed,
>
> I tried both javac 1.6.0_05 and 1.6.0_21 and both give me the same
> error.
>
> % javac -version
>          javac 1.6.0_05
>
>
> % ant clean
> Buildfile: build.xml
>
> -load.properties:
>
> clean:
>     [delete] Deleting directory /lscratch/apps/BioMart8/test_he/dist
>     [delete] Deleting directory /lscratch/apps/BioMart8/test_he/build
>
> BUILD SUCCESSFUL
> Total time: 0 seconds
>
>
>
> % ant
> Buildfile: build.xml
>
> -load.properties:
>
> -init:
>      [mkdir] Created dir:
> /lscratch/apps/BioMart8/test_he/build/classes/main/META-INF
>      [mkdir] Created dir:
> /lscratch/apps/BioMart8/test_he/build/classes/start
>      [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/build/lib
>      [mkdir] Created dir:
/lscratch/apps/BioMart8/test_he/dist/web/work

>      [mkdir] Created dir: /lscratch/apps/BioMart8/test_he/dist/logs
>      [mkdir] Created dir:
> /lscratch/apps/BioMart8/test_he/dist/registry/linkindices
>
> compile.main:
>      [javac] Compiling 451 source files to
> /lscratch/apps/BioMart8/test_he/build/classes/main
>      [javac] ----------
>      [javac] 1. ERROR in
>
/lscratch/apps/BioMart8/test_he/src/org/biomart/api/enums/BiomartVersion

> .java (at line 1)
>      [javac]     package org.biomart.api.enums;
>      [javac]     ^^
>      [javac] The type Enum is not generic; it cannot be parameterized
> with arguments<BiomartVersion>
>      [javac] ----------
>      [javac] 1 problem (1 error)
>
> BUILD FAILED
> /lscratch/apps/BioMart8/test_he/build.xml:24: Compile failed; see the
> compiler error output for details.
>
> -----Original Message-----
> From: Syed Haider [mailto:[hidden email]]
> Sent: Wednesday, February 09, 2011 4:44 PM
> To: Estrella, Heather
> Cc: [hidden email]
> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
when

> run ant
>
> Right, my suspicion is the java compile (javac). It seems to be an old
> java. By any chance, do you a non-eclipse version of javac and that is
> javac 1.6?
>
>
>
> On 10/02/2011 00:20, Estrella, Heather wrote:
>> I was just thinking the same thing because I got the same error with
> the
>> newly downloaded code.
>>
>> -bash-3.2$ java -version
>> java version "1.6.0_05"
>> Java(TM) SE Runtime Environment (build 1.6.0_05-b13)
>> Java HotSpot(TM) 64-Bit Server VM (build 10.0-b19, mixed mode)
>>
>> -bash-3.2$ javac -version
>> Eclipse Java Compiler v_677_R32x, 3.2.1 release, Copyright IBM Corp
>> 2000, 2006. All rights reserved.
>>
>> -bash-3.2$ ant -version
>> Apache Ant version 1.6.5 compiled on January 6 2007
>>
>> -----Original Message-----
>> From: Syed Haider [mailto:[hidden email]]
>> Sent: Wednesday, February 09, 2011 4:25 PM
>> To: Estrella, Heather
>> Cc: [hidden email]
>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
> when
>> run ant
>>
>> let me have the output of these:
>>
>> java -version
>> javac -version
>> ant -version
>>
>>
>> On 10/02/2011 00:15, Estrella, Heather wrote:
>>> I just get the Enum error. I just tried re-downloading a clean
> version
>>> of rc4 to see if I can get that to run a little more smoothly. The
>>> install that we had is pretty much messed up until the java
>> compilation
>>> error is resolved.
>>>
>>> Here's the exact sequence of commands I've run:
>>>
>>> svn update
>>> ant clean
>>> ant
>>>
>>> I've tried re-running them in that sequence and here's the output:
>>>
>>> -bash-3.2$ svn update
>>>       At revision 7145.
>>>
>>> -bash-3.2$ ant clean
>>>       Buildfile: build.xml
>>>
>>>       -load.properties:
>>>
>>>       clean:
>>>          [delete] Deleting directory
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist
>>>          [delete] Deleting directory
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build
>>>
>>>       BUILD SUCCESSFUL
>>>
>>> -bash-3.2$ ant
>>>       Buildfile: build.xml
>>>
>>>       -load.properties:
>>>
>>>       -init:
>>>           [mkdir] Created dir:
>>>
> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main/META-INF
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/start
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/lib
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/web/work
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/logs
>>>           [mkdir] Created dir:
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/dist/registry/linkindices
>>>
>>>       compile.main:
>>>           [javac] Compiling 455 source files to
>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>           [javac] ----------
>>>           [javac] 1. ERROR in
>>>
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/api/enums/Ope

>>> ration.java (at line 1)
>>>           [javac]     package org.biomart.api.enums;
>>>           [javac]     ^^
>>>           [javac] The type Enum is not generic; it cannot be
>>> parameterized with arguments<Operation>
>>>       [javac] ----------
>>>
>>>           [javac] 1 problem (1 error)
>>>
>>>       BUILD FAILED
>>>       /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32:
Compile

>>> failed; see the compiler error output for details.
>>>
>>>       Total time: 1 second
>>>
>>>
>>> -----Original Message-----
>>> From: Syed Haider [mailto:[hidden email]]
>>> Sent: Wednesday, February 09, 2011 4:16 PM
>>> To: Estrella, Heather
>>> Cc: [hidden email]
>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>> when
>>> run ant
>>>
>>> You need to run:
>>>
>>> ant
>>>
>>> after ant clean.
>>>
>>> then it will recreate the dist/
>>>
>>> and then run:
>>>
>>> ./dist/scripts/biomart-server.sh start
>>>
>>>
>>>
>>>
>>> On 10/02/2011 00:07, Estrella, Heather wrote:
>>>> Thanks Syed,
>>>>
>>>> When I ran the 'ant clean' the first time, it deleted the dist
>>> directory
>>>> and the only place I could find the biomart-server.sh script is now
>> in
>>>> the scripts directory located at $BIOMART_HOME
>>>>
>>>> bash-3.2$ ant clean
>>>> Buildfile: build.xml
>>>>
>>>> -load.properties:
>>>>
>>>> clean:
>>>>
>>>> BUILD SUCCESSFUL
>>>> Total time: 0 seconds
>>>>
>>>> Here's a list of the BIOMART_HOME directory contents. "ant clean"
>>> really
>>>> changed the directory structure from what I was previously used to
>>> (i.e.
>>>> dist/scripts, etc.). because there is now a "plugins" directory is
>> why
>>> I
>>>> thought maybe "svn update" updated my original rc3 installation to
>>> rc4.
>>>> However, even in the rc4 install that we have, there is still the
>> dist
>>>> directory so I don't know what's going on.
>>>> ant.properties
>>>> build_test.xml
>>>> build.xml
>>>> conf
>>>> ext
>>>> images
>>>> lib
>>>> plugins
>>>> registry
>>>> scripts
>>>> src
>>>> start
>>>> test
>>>> testdata
>>>> voldemort
>>>> web
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Syed Haider [mailto:[hidden email]]
>>>> Sent: Wednesday, February 09, 2011 4:08 PM
>>>> To: Estrella, Heather
>>>> Cc: [hidden email]
>>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>>> when
>>>> run ant
>>>>
>>>> Heather,
>>>>
>>>> 1- please send me the console output when you run 'ant'
>>>>
>>>> 2- to start/stop biomart server, the commands are:
>>>>
>>>> ./dist/scripts/biomart-server.sh stop
>>>> ./dist/scripts/biomart-server.sh start
>>>>
>>>> thats from the dist directory. let me know if that helps.
>>>>
>>>> Syed
>>>>
>>>> On 09/02/2011 23:56, Estrella, Heather wrote:
>>>>> Thanks Syed,
>>>>>
>>>>> That got me past the ant problem. However, it looks like running
> svn
>>>>> update automatically took my rc3 code to rc4.
>>>>>
>>>>> I'm trying to start my biomart server back up using "
>>>>> ./scripts/biomart-server.sh start" and I get the following error:
>>>>>     ** ERROR:
>>>>> /lscratch/apps/BioMart8/rc3/trunk/scripts/biomart-start.jar is not
>>>>> readable!
>>>>>
>>>>> This jar file doesn't exist in the scripts directory. It isn't
> found
>>>>> anywhere in the installation path.
>>>>>
>>>>> Here is a list of what is in the scripts directory:
>>>>> biomart-server.bat
>>>>> build.sh
>>>>> fasta.sh
>>>>> jetty.bat
>>>>> Jetty-Service.exe
>>>>> martconfigurator.bat
>>>>> martrunner.bat
>>>>> prunmgr.exe
>>>>> runSoakTest.sh
>>>>> biomart-server.sh
>>>>> fasta.bat
>>>>> generate-password.sh
>>>>> jetty-service.conf
>>>>> launch.sh
>>>>> martconfigurator.sh
>>>>> martrunner.sh
>>>>> prunsrv.exe
>>>>> test.sh
>>>>>
>>>>> Also, can you please point me to the documentation is located? I'm
>>>> kinda
>>>>> running blind.
>>>>>
>>>>> Thanks,
>>>>> Heather
>>>>>
>>>>> -----Original Message-----
>>>>> From: Syed Haider [mailto:[hidden email]]
>>>>> Sent: Wednesday, February 09, 2011 3:47 PM
>>>>> To: Estrella, Heather
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [BioMart Users] svn update for rc3 get compiler error
>>>> when
>>>>> run ant
>>>>>
>>>>> Heather,
>>>>>
>>>>> try:
>>>>>         ant clean
>>>>> and then
>>>>>         ant
>>>>>
>>>>> also, please make sure you are running the above commands from the
>>>>> following directory:
>>>>>
>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/
>>>>>
>>>>> thanks
>>>>> Syed
>>>>>
>>>>> On 09/02/2011 23:36, Estrella, Heather wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to upgrade my RC3 installation to the new RC3 code
that

>>>>> fixes the copy/paste URL bug. I ran
>>>>>>
>>>>>> svn update
>>>>>>
>>>>>> ant
>>>>>>
>>>>>> When I ran ant, I received the following compiler error:
>>>>>>
>>>>>> Buildfile: build.xml
>>>>>>
>>>>>> -load.properties:
>>>>>>
>>>>>> -init:
>>>>>>
>>>>>> compile.main:
>>>>>>
>>>>>>           [javac] Compiling 114 source files to
>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build/classes/main
>>>>>>
>>>>>>           [javac] ----------
>>>>>>
>>>>>>           [javac] 1. ERROR in
>>>>>
>>>>
>>>
>>
>
/lscratch/apps/BioMart8/trunk_jan_26/trunk/src/org/biomart/configurator/

>>>>> utils/McGuiUtils.java (at line 1)
>>>>>>
>>>>>>           [javac]     package org.biomart.configurator.utils;
>>>>>>
>>>>>>           [javac]     ^^
>>>>>>
>>>>>>           [javac] The type Enum is not generic; it cannot be
>>>> parameterized
>>>>> with arguments<McGuiUtils>
>>>>>>
>>>>>>           [javac] ----------
>>>>>>
>>>>>>           [javac] 1 problem (1 error)
>>>>>>
>>>>>> BUILD FAILED
>>>>>>
>>>>>> /lscratch/apps/BioMart8/trunk_jan_26/trunk/build.xml:32: Compile
>>>>> failed; see the compiler error output for details.
>>>>>>
>>>>>> This is the portion of the McGuiType.java script that is having
>>>> issues
>>>>>>
>>>>>> ...
>>>>>>
>>>>>> /**
>>>>>>
>>>>>>        * this class should not be used for web, should only be
used

>> for
>>>>>>
>>>>>>        * MartConfigurator GUI.
>>>>>>
>>>>>>        */
>>>>>>
>>>>>> public enum McGuiUtils {
>>>>>>
>>>>>>               INSTANCE;
>>>>>>
>>>>>>               private McGuiType guiType;
>>>>>>
>>>>>> ...
>>>>>>
>>>>>> What am I missing?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Heather
>>>>>>
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