[Neurodebian-users] Problem with MIPAV

Fri Dec 14 15:58:13 UTC 2012

2012/12/14 Yaroslav Halchenko <debian at onerussian.com>:

> sorry about the delay, Lorenzo

No problem Yaroslav, thank you for your answer.

>> With -v, I get several java errors which I'm not posting since I think
>> it is more an upstream problem.
>
> who knows who knows... showing the error could have given a hint

Ok then :) Here you go:

Verbose mode

 MIPAV_BASE    = /usr/share/mipav
 MIPAV_JAR     =
Uninstall-MIPAV/uninstaller.jar:InsightToolkit/lib/InsightToolkit/InsightToolkit.jar:lib/axiom-api-1.2.4.jar:lib/commons-codec-1.3.jar:lib/ACCESSION_client_VTool.jar:lib/iText-2.0.7.jar:lib/pdfbox-1.2.0.jar:lib/axiom-dom-1.2.4.jar:lib/jj2kpack.jar:lib/rampart-trust-1.2.jar:lib/WildMagic.jar:lib/JimiProClasses.jar:lib/commons-httpclient-3.0.1.jar:lib/fontbox-1.2.0.jar:lib/rampart-policy-1.2.jar:lib/tar.jar:lib/junit-4.4.jar:lib/jempbox-1.2.0.jar:lib/jaxp/xercesImpl.jar:lib/jaxp/xalan.jar:lib/jaxp/sax.jar:lib/jaxp/dom.jar:lib/jaxen-1.1-beta-10.jar:lib/jax-qname.jar:lib/XmlSchema-1.3.1.jar:lib/wss4j-1.5.2.jar:lib/wstx-asl-3.2.1.jar:lib/commons-logging-1.1.1.jar:lib/bcprov-jdk15-136.jar:lib/axis2-kernel-1.2.jar:lib/jdom.jar:lib/axiom-impl-1.2.4.jar:lib/jhall.jar:lib/wsdl4j-1.6.2.jar:lib/neethi-2.0.1.jar:lib/xmlsec-1.4.0.jar:lib/rampart-core-ndar-1.2.jar:lax.jar:help/mipav_help.jar
 MIPAV_JAVA    = /usr/bin/java
 MIPAV_LOG     = -
 MIPAV_PLUGINS =
/home/lorenzo/mipav/:/home/lorenzo/mipav/plugins/:/usr/share/mipav/plugins/
 MIPAV_MEMORY  = 256M
 MIPAV_ARG     = -pluginDir /usr/share/mipav/plugins/

HasRunBefore: null
Exception during event dispatch:
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
   at java.util.ArrayList.raiseBoundsError(libgcj.so.13)
   at java.util.ArrayList.checkBoundExclusive(libgcj.so.13)
   at java.util.ArrayList.set(libgcj.so.13)
   at javax.swing.text.html.StyleSheet.resolveStyle(libgcj.so.13)
   at javax.swing.text.html.StyleSheet.getResolvedStyle(libgcj.so.13)
   at javax.swing.text.html.StyleSheet.getRule(libgcj.so.13)
   at javax.swing.text.html.ViewAttributeSet.<init>(libgcj.so.13)
   at javax.swing.text.html.StyleSheet.getViewAttributes(libgcj.so.13)
   at javax.swing.text.html.ParagraphView.getAttributes(libgcj.so.13)
   at javax.swing.text.html.ParagraphView.setPropertiesFromAttributes(libgcj.so.13)
   at javax.swing.text.html.ParagraphView.setParent(libgcj.so.13)
   at javax.swing.text.CompositeView.replace(libgcj.so.13)
   at javax.swing.text.BoxView.replace(libgcj.so.13)
   at javax.swing.text.html.BlockView.replace(libgcj.so.13)
   at javax.swing.text.CompositeView.loadChildren(libgcj.so.13)
   at javax.swing.text.CompositeView.setParent(libgcj.so.13)
   at javax.swing.text.html.BlockView.setParent(libgcj.so.13)
   at javax.swing.text.CompositeView.replace(libgcj.so.13)
   at javax.swing.text.BoxView.replace(libgcj.so.13)
   at javax.swing.text.html.BlockView.replace(libgcj.so.13)
   at javax.swing.text.CompositeView.loadChildren(libgcj.so.13)
   at javax.swing.text.CompositeView.setParent(libgcj.so.13)
   at javax.swing.text.html.BlockView.setParent(libgcj.so.13)
   at javax.swing.plaf.basic.BasicTextUI$RootView.setView(libgcj.so.13)
   at javax.swing.plaf.basic.BasicTextUI.setView(libgcj.so.13)
   at javax.swing.plaf.basic.BasicTextUI.modelChanged(libgcj.so.13)
   at javax.swing.plaf.basic.BasicTextUI$Handler.propertyChange(libgcj.so.13)
   at java.beans.PropertyChangeSupport.firePropertyChange(libgcj.so.13)
   at java.beans.PropertyChangeSupport.firePropertyChange(libgcj.so.13)
   at java.awt.Component.firePropertyChange(libgcj.so.13)
   at javax.swing.text.JTextComponent.setDocument(libgcj.so.13)
   at javax.swing.JEditorPane.setEditorKit(libgcj.so.13)
   at javax.swing.JEditorPane.setContentType(libgcj.so.13)
   at javax.swing.JEditorPane.getStream(libgcj.so.13)
   at javax.swing.JEditorPane.setPage(libgcj.so.13)
   at StartMipav.Screen1(StartMipav.java:100)
   at StartMipav.hasRunBefore(StartMipav.java:71)
   at StartMipav.access$200(StartMipav.java:39)
   at StartMipav$4.run(StartMipav.java:576)
   at java.awt.event.InvocationEvent.dispatch(libgcj.so.13)
   at java.awt.EventQueue.dispatchEvent(libgcj.so.13)
   at java.awt.EventDispatchThread.run(libgcj.so.13)

NB.  "find / -type f -name libgcj.so.13" finds nothing on my system.

>> My questions are:
>
>> 1. Are there any plans to update mipav to this release anytime soon?
>
> good news are:   MIPAV is finally open-sourced and proper Debian
>   packaging is possible now (currently it is just a "downloader" of the
>   binary MIPAV distribution)
>
> not so good news:  there is no specific timeline yet for the work
>   on such a proper package.  We definitely are interested to help and
>   there is interest "upstream" but no date could be guaranteed/set.
>   (myself I am not even using MIPAV... more of a Python guy)

Oh, finally they released the project open source! That's awesome!

Well, if I can help in some way (testing? I'm starting to read
something about debian packaging, but I don't think I'll be able to
package anything in the short term) I'd be glad to.

>>  Anyway, before reporting upstream, I would like to try to install the
>> latest mipav release, which is 6.0.1 (2012-11-14).
>
> since our installer package is pretty much just a 'downloader' for
> the binary distribution -- indeed you might better off just following
> stock upstream installation instructions for now

I'll try this way. I usually try to avoid to install things manually
because I don't want to risk to bork my system with files unknown to
apt (happened in the past :) ).

> by default we have deb-src lines in
> /etc/apt/sources.list.d/neurodebian.sources.list are simply
> commented out -- uncomment them, and run apt-get update

Uhm, that's what I did:

root at linux-laptop:~# cat /etc/apt/sources.list.d/neurodebian.sources.list
deb http://www.neuro.webdisk.com.ua data main contrib non-free
deb-src http://www.neuro.webdisk.com.ua data main contrib non-free
deb http://www.neuro.webdisk.com.ua wheezy main contrib non-free
deb-src http://www.neuro.webdisk.com.ua wheezy main contrib non-free

root at linux-laptop:~# apt-get update
[snip]

root at linux-laptop:~# apt-get source mipav
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to find a source package for mipav

I guess I'm missing something here :S

> but once again -- it would be just a downloader package for binary
> distribution of MIPAV prepared by Bennett (CCed) and there is no newer
> version seems to be avail on http://www.nitrc.org/frs/?group_id=228

Indeed, my plan was to modify the package to fetch the binary for the
latest release leaving the rest unchanged as far as possible (apart
from the name) :) One of the problem I encountered was that I didn't
know how to get a url to download the package from...

Thanks again,

Lorenzo