Re: [base] update issue from 2.14.0 to 2.16.1

2010-11-24 Thread philipp-1 . kaiser
Oh, silly me. Thanks for pointing at the right direction. Obviously I 
forgot to set the right environment for the update procedure.
For Solaris it's necessary to have this old java version for some os 
components, otherwise I would have updated the java completely.

Thank you for BASE
/philipp--
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Re: [base] update issue from 2.14.0 to 2.16.1

2010-11-24 Thread Olivier Lefevre
 I guess we really should change the compilation 
 to use '-target 1.6'

Or simply omit it. In general I can think of few scenarios
where you'd want to target an older VM than the one you are
working with (one reason might be compiler fixes that were
not back-ported): that invites the sort of errors the OP 
ran into, unless the developer is extremely careful not to
use any of the newer functionality.

-- O.L.


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Re: [base] update issue from 2.14.0 to 2.16.1

2010-11-24 Thread Nicklas Nordborg
On 2010-11-24 15:10, Olivier Lefevre wrote:
 I guess we really should change the compilation
 to use '-target 1.6'

 Or simply omit it. In general I can think of few scenarios
 where you'd want to target an older VM than the one you are
 working with (one reason might be compiler fixes that were
 not back-ported): that invites the sort of errors the OP
 ran into, unless the developer is extremely careful not to
 use any of the newer functionality.


I investigated the history of this a bit further and the story is like this:

BASE 2.5 only worked with java 1.5 but not with 1.6 due to some issues 
with webservices. We were developing with 1.5.

We started to use java 1.6 for development during BASE 2.6 but still 
wanted to keep support for java 1.5 since no Mac version of 1.6 existed 
(we had two developers using Mac). This is when the target 1.5 was 
added to the build.

BASE 2.7 dropped official support for java 1.5 but nobody though of 
changing the target attribute. I have done this today so it will be 
fixed in the next BASE release.

/Nicklas


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[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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