[Biojava-dev] JAXB plugin dependencies in sequence-blastxml module

[trevor paterson (RI)]

I managed to fix the Archiva configuration by adding '**/*' to the whitelist for http://download.java.net/maven/2/
Somehow available artifacts had been added to the whitelist (in my world you would expect unavailable artifacts to be added to the blacklist...;)

So I can almost get the whole project to compile on linux/netbeans

The remaining bug is with the jaxb-api, the pom includes v2.2 as a dependency, but netbeans seems to have an internal version of v2.0 which it bootstraps with - so wont use 2.2 ( as far as I can tell java1.6 includes v2.2 - but as an internal ??runtime only?? Library)

I am trying to kill this somehow - or put the correct version in lib/endorsed

Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk

Bioinformatics 
The Roslin Institute
Edinburgh University
Scotland EH25 9PS
phone +44 (0)131 5274402
http://www.roslin.ed.ac.uk
http://www.comparagrid.org
http://www.thearkdb.org

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-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI)
Sent: 04 September 2009 12:00
To: 'biojava-dev at biojava.org'
Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module

Apologies

It looks like we are failing to get these dependencies because we use a local Archiva repository to mirror the external world.... and for some reason it is failing to pull down these dependencies which have checksum failures ( even though Archiva is set to Ignore checksum failures )

When we don't use archiva as a mirror we can get the dependencies...

Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk

Bioinformatics 
The Roslin Institute
Edinburgh University
Scotland EH25 9PS
phone +44 (0)131 5274402
http://www.roslin.ed.ac.uk
http://www.comparagrid.org
http://www.thearkdb.org

Please consider the environment before printing this e-mail

The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336
Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. 


-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of trevor paterson (RI)
Sent: 04 September 2009 11:29
To: 'biojava-dev at biojava.org'
Subject: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module


Hi Andreas

I have been looking at compiling the maven project with Andy and am getting stuck at the maven-jaxb2-plugin specified for the sequence-balstxml module

This is lacking a required version identifier - ( I seem to recall that only core maven plugins can skip the version)

I tried a couple of the available plugins (see http://download.java.net/maven/2/org/jvnet/jaxb2/maven2/maven-jaxb2-plugin/ )

But these were failing for other non standard artifact dependencies..

e.g version 0.6.0
  Path to dependency:
          1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0
          2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.6
          3) org.kohsuke.rngom:rngom:jar:20061207
  Path to dependency:
          1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.6.0
          2) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.2.4

e.g version 0.7.1
  Path to dependency:
          1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1
          2) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin-raw:jar:0.7.1
          3) org.jfrog.maven.annomojo:maven-plugin-anno:jar:1.3.1
  Path to dependency:
          1) org.jvnet.jaxb2.maven2:maven-jaxb2-plugin:maven-plugin:0.7.1
          2) org.jvnet.jaxb2_commons:jaxb-xjc:jar:2.1.10
          3) org.kohsuke.rngom:rngom:jar:20061207

Which version of the maven-jaxb2-plugin should the build be using?

And am I missing a required repository for the dependencies for the maven-jaxb2-plugin

Or is it necessary to find these dependencies manually and install them locally?

We are currently configured system wide to use the following repos ( and whatever plugin repos etc you add in project POMs)

Central Repository http://repo1.maven.org/maven2

Java.net Repository http://download.java.net/maven/2/

Netbeans Repository http://deadlock.netbeans.org/maven2/

Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk<mailto:trevor.paterson at roslin.ed.ac.uk>

Bioinformatics
The Roslin Institute
Edinburgh University
Scotland EH25 9PS
phone +44 (0)131 5274402
http://www.roslin.ed.ac.uk<http://www.roslin.ed.ac.uk/>
http://www.comparagrid.org<http://www.comparagrid.org/>
http://www.thearkdb.org<http://www.thearkdb.org/>

Please consider the environment before printing this e-mail

The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336
Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.


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