Re: [micro-manager-general] Linux installation

[Jörg H. <joe...@un...>]

Thanks for all the answers. We made some progress, namely:

1. We were trying to install micro-manager on two computers, on my 
private laptop running ubuntu, from source, and on the desktop machine 
(also ubuntu) that will eventually be used for the real work, using the 
.deb files.

2.  Installation of the binaries worked well, when using the debian 
package of ImageJ plus the two appropriate micromanager .deb files 
("details: debian/ubuntu micromanager with debian/ubuntu 
ImageJ")---thanks for the instructions (and the new README file!).

3. Building from source, creating the dir "/usr/lib/micro-manager" 
helped in the sense that the whole sequence from ./mmUnixBuild.sh to 
"make install" and "ldconfig" did run without errors. But:

I then started ImageJ ("./run &") -- ImageJ starts up.  Micromanager is 
in the plugin menue, I open Micro-manager Studio, the registration 
window opens, and then the micro-manager window, but no Micro-manager 
startup configuration.  On the terminal I got the error messages added 
at the bottom of this mail*. In addition, ImageJ and Micromanager 
couldn't be closed any more.

Essentially the same happened when we tried to install the binaries 
using the "details: debian/ubuntu micromanager with custom ImageJ or Fiji").

I then removed /usr/local/ImageJ and installed the ImageJ debian package 
(imagej_1.43b-1_all.deb), followed by building of micromanager from 
source (including moving the beanshell and swingx files from classext to 
the plugins folder).  Installation again seemed to work, but again, when 
starting micro-manager from ImageJ, no splash screen for the 
configuration file appeared. When I tried to load the demo file from the 
micromanager window, I got:
Exception occurred:java.lang.NullPointerException

Although we now have a working installation, I think it would be a good 
idea to clear up the problems I had with the alternative methods.

Answers to other suggestions and questions in the thread:
- I was of course installing as su, and the shell is bash
- The swingx that didn't work was from "swinglabs.org/downloads.jsp
- I didn't need ACE, as I had libace and libace-dev (didn't originally 
know whether you needed ACE as well)

Thanks again, Jörg


*Messages after starting micro-manager built from source:
(<unknown>:3530): Gtk-CRITICAL **: gtk_paint_box: assertion 
`style->depth == gdk_drawable_get_depth (window)' failed
Native code library failed to load.
java.lang.UnsatisfiedLinkError: no MMCoreJ_wrap in java.library.path
Exception in thread "AWT-EventQueue-0" java.lang.UnsatisfiedLinkError: 
mmcorej.MMCoreJJNI.swig_module_init()V
    at mmcorej.MMCoreJJNI.swig_module_init(Native Method)
    at mmcorej.MMCoreJJNI.<clinit>(MMCoreJJNI.java:487)
    at mmcorej.CMMCore.<init>(CMMCore.java:37)
    at 
org.micromanager.MMStudioMainFrame$43.windowOpened(MMStudioMainFrame.java:1192)
    at 
java.awt.AWTEventMulticaster.windowOpened(AWTEventMulticaster.java:322)
    at java.awt.Window.processWindowEvent(Window.java:1842)
    at javax.swing.JFrame.processWindowEvent(JFrame.java:279)
    at java.awt.Window.processEvent(Window.java:1803)
    at java.awt.Component.dispatchEventImpl(Component.java:4501)
    at java.awt.Container.dispatchEventImpl(Container.java:2081)
    at java.awt.Window.dispatchEventImpl(Window.java:2458)
    at java.awt.Component.dispatchEvent(Component.java:4331)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
    at 
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
    at 
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at 
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

(<unknown>:3530): Gtk-CRITICAL **: gtk_paint_box: assertion 
`style->depth == gdk_drawable_get_depth (window)' failed

(<unknown>:3530): Gtk-CRITICAL **: gtk_paint_box: assertion 
`style->depth == gdk_drawable_get_depth (window)' failed
Jul 7, 2009 11:23:04 AM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush system prefs: 
java.util.prefs.BackingStoreException: /etc/.java/.systemPrefs/org 
create failed.

-- 
Prof. Jörg Hagmann-Zanolari MD
University of Basel
Department of Biomedicine
Institute of Biochemistry and Genetics
Mattenstrasse 28
CH-4058 Basel
Switzerland
Phone +41 (0)61 267 3565