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:[email protected]] Sent: Wednesday, February 09, 2011 5:26 PM To: Estrella, Heather Cc: [email protected]; 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:[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
