[base] update issue from 2.14.0 to 2.16.1

2010-11-23 Thread philipp-1 . kaiser
Dear team,

I got a weird error during updating my base2 installation from 2.14.0 to 
2.16.1.
Tomcat is shut down, I run sh updatedb.sh password.
See the output below.

Any advise or idea whats going on?
Thanks in advance,
/philipp

[0%]--System information-
BASE : 2.16.1
Database : 
jdbc:mysql://localhost/base2?characterEncoding=UTF-8useCursorFetch=truedefaultFetchSize=100useServerPrepStmts=true
Dialect  : org.hibernate.dialect.MySQLInnoDBDialect
JDBC : com.mysql.jdbc.Driver; version 5.1
Java : Java(TM) Platform, Standard Edition for Business; 1.5.0_16-b02; 
Sun Microsystems Inc.
OS   : SunOS; x86; 5.10
-
[0%]Building database...
[30%]   Database built successfully.
[35%]   Initialising database...
[36%]   --Creating quota types...
[37%]   --Creating quota...
[38%]   --Creating roles...
[39%]   --Creating users...
[40%]   --Creating groups...
[41%]   --Creating keys...
[42%]   --Creating units...
[43%]   --Creating protocol types...
[44%]   --Creating hardware types...
[45%]   --Creating hardware...
[46%]   --Creating software types...
[47%]   --Creating software...
[48%]   --Creating directories...
[49%]   --Creating file types...
[50%]   --Creating MIME types...
[50%]   --Creating plate geometries...
[51%]   --Creating plate mappings...
[52%]   --Creating bioplate types...
[53%]   --Creating labels...
[54%]   --Creating annotation types...
[56%]   --Creating clients...
[57%]   --Creating plugin definitions...
[58%]   --Creating example plugin configurations...
[59%]   --Creating formulas...

java.lang.NoSuchMethodError: 
java.util.Arrays.copyOf([Ljava/lang/Object;I)[Ljava/lang/Object;
at 
net.sf.basedb.core.IntensityFormula.getExpressions(IntensityFormula.java:91)
at net.sf.basedb.core.Install.initDatabase(Install.java:757)
at net.sf.basedb.install.InitDB.main(InitDB.java:74)--
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Re: [base] update issue from 2.14.0 to 2.16.1

2010-11-23 Thread Olivier Lefevre
 Java     : Java(TM) Platform,
 Standard Edition for Business; 1.5.0_16-b02; Sun Microsystems Inc.

 java.lang.NoSuchMethodError: 
 java.util.Arrays.copyOf([Ljava/lang/Object;I)[Ljava/lang/Object;

You're running Java 1.5 but the Array.copyOf methods were
introduced in Java 1.6:
http://download.oracle.com/javase/6/docs/api/java/util/Arrays.html#copyOf%28T[],%20int%29
I'm surprised this didn't cause an incompatibility error
earlier, though.

-- O.L.


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Re: [base] update issue from 2.14.0 to 2.16.1

2010-11-23 Thread Olivier Lefevre
 That line of code (IntensityFormula.java:91) was changed in
 2.16 so it is not so strange.

I meant I was surprised that this 1.5 VM didn't immediately
reject classes obviously compiled against 1.6. Did you use
the -target 1.5 option in compilation?

-- O.L.


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Re: [base] update issue from 2.14.0 to 2.16.1

2010-11-23 Thread Nicklas Nordborg
On 2010-11-23 21:22, Olivier Lefevre wrote:
 That line of code (IntensityFormula.java:91) was changed in
 2.16 so it is not so strange.

 I meant I was surprised that this 1.5 VM didn't immediately
 reject classes obviously compiled against 1.6. Did you use
 the -target 1.5 option in compilation?


Ahh... yes actually we have that.. I have tried to investigate why and 
it seems to be related with BASE version around 2.5-2.7 
(http://base.thep.lu.se/ticket/899). There was a period when we had to 
support java 1.5 even though we used java 1.6 for development. Since 
that is no longer the case I guess we really should change the 
compilation to use '-target 1.6'. Thanks for pointing it out.

/Nicklas

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