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:[email protected]]
Sent: Wednesday, February 09, 2011 4:44 PM
To: Estrella, Heather
Cc: [email protected]
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:[email protected]]
> Sent: Wednesday, February 09, 2011 4:25 PM
> To: Estrella, Heather
> Cc: [email protected]
> 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:[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
>>>>>
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
