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
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