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: [email protected] [mailto:[email protected]] On Behalf Of Estrella, Heather Sent: Wednesday, February 09, 2011 4:21 PM To: Syed Haider Cc: [email protected] 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:[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 _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
