[Biojava-dev] JAXB plugin dependencies in sequence-blastxml module
trevor paterson (RI)
trevor.paterson at roslin.ed.ac.uk
Fri Sep 4 16:12:47 UTC 2009
[ONLY OF INTEREST TO NETBEANS USERS]
I can't find a way to configure Netbeans6.5 to not use its bundled jaxb-api, so am having to use the endorsed libraries route....
Until netbeans 6.7 (which is allegedly still flakey) you can't alter the jdk for maven to use by default, it just uses whatever JAVA_HOME is.
You can however add a -D property flag to any global or custom maven action.
So you can either set to build with a different jdk (containing your endorsed libraries)
Or you can just point at the ensdorsed libraries location itself
i.e.
-DEnv.JAVA_HOME=/nfs_netapp/paterson/MyJava6/jdk1.6.0_04/
-Djava.endorsed.dirs= /nfs_netapp/paterson/MyJava6/jdk1.6.0_04/jre/lib/endorsed
You don't seem to be able to add these as as maven properties in a POM or settings.xml
And I am not sure why andy is not getting this happenning in his OSX.5/MACJava worl - probably he has not installed some netbeans plugin module that wired in this jaxb version
Trevor
-----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 15:14
To: 'biojava-dev at biojava.org'
Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module
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
-----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
-----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/>
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