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:[email protected]]
Sent: Wednesday, February 09, 2011 4:16 PM
To: Estrella, Heather
Cc: [email protected]
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:[email protected]]
> Sent: Wednesday, February 09, 2011 4:08 PM
> To: Estrella, Heather
> Cc: [email protected]
> 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:[email protected]]
>> Sent: Wednesday, February 09, 2011 3:47 PM
>> To: Estrella, Heather
>> Cc: [email protected]
>> 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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