ImageJ fails to run - /usr/share/imagej/jni/*: No such file or directory

[Thomas Ibbotson]

Binary package hint: imagej

When trying to run imagej on a fresh install of Karmic the following error message is produced:

Open other images in this ImageJ panel as follows:
  imagej -p 1 <image1> [<image2> ... <imageN>]

cat: /usr/share/imagej/jni/*: No such file or directory
/usr/bin/imagej: line 418: //bin/java: No such file or directory

which shows 2 problems. The first is the problem I am reporting here. The 2nd can be worked around by setting the JAVA_HOME environment variable appropriately.

imagej:
  Installed: 1.43b-1ubuntu1
  Candidate: 1.43b-1ubuntu1
  Version table:
 *** 1.43b-1ubuntu1 0
        500 http://mirror.ox.ac.uk karmic/universe Packages
        100 /var/lib/dpkg/status

Steps to reproduce:
1. Install imagej: "sudo apt-get install imagej"
2. Run imagej from a command-line: "imagej"

Also if I set the JAVA_HOME variable correctly, I get the following error message:

Open other images in this ImageJ panel as follows:
  imagej -p 1 <image1> [<image2> ... <imageN>]

cat: /usr/share/imagej/jni/*: No such file or directory
Exception in thread "main" java.awt.AWTError: Cannot load AWT toolkit: gnu.java.awt.peer.gtk.GtkToolkit
   at java.awt.Toolkit.getDefaultToolkit(libgcj.so.10)
   at java.awt.Font.tk(libgcj.so.10)
   at java.awt.Font.getPeerFromToolkit(libgcj.so.10)
   at java.awt.Font.<init>(libgcj.so.10)
   at ij.ImageJ.<clinit>(ImageJ.java:75)
   at java.lang.Class.initializeClass(libgcj.so.10)
Caused by: java.lang.UnsatisfiedLinkError: libgtkpeer: libgtkpeer.so: cannot open shared object file: No such file or directory
   at java.lang.Runtime._load(libgcj.so.10)
   at java.lang.Runtime.loadLibrary(libgcj.so.10)
   at java.lang.System.loadLibrary(libgcj.so.10)
   at gnu.java.awt.peer.gtk.GtkToolkit.<clinit>(libgcj.so.10)
   at java.lang.Class.initializeClass(libgcj.so.10)
   at java.lang.Class.forName(libgcj.so.10)
   at java.awt.Toolkit.getDefaultToolkit(libgcj.so.10)
   ...5 more

[Lucio (lumatemp-nospam)]

Same here. Most important to me is that the graphic frontend does not start at all (in Ubuntu 9.04 it was working)

[linuxed (linuxed)]

If anyone's looking for a temporary fix to get imagej working in Karmic you can use the following.

sudo gedit /usr/bin/imagej

Copy and paste the following on the 2nd line. Save the file when finished.

# run the program and exit
if [ ! -e "$HOME/.imagej/ij.jar" ] ; then
    if [ ! -e "$HOME/.imagej" ] ; then
        mkdir $HOME/.imagej
        cp -P -R /usr/share/imagej/* $HOME/.imagej
    fi
    cp -P /usr/share/java/ij.jar $HOME/.imagej
fi
java -jar $HOME/.imagej/ij.jar
exit 0

[blab_blab (blab-blab)]

I had the same issue.

After a while I found:
http://packages.ubuntu.com/karmic/imagej
which made me try to install “java2-runtime” (http://packages.ubuntu.com/karmic/java2-runtime)

I've updated/installed: default-jre, gcj-4.4-jre, gcj-jre and openjdk-6-jre via synaptic (don't ask me why), and luckily ImageJ works fine.

[rCX (rcx)]

blab_blab's suggestion...

sudo apt-get install default-jre gcj-4.4-jre gcj-jre openjdk-6-jre

...worked perfectly for me in ubuntu 9.10.

[Carnë Draug (carandraug)]

I solved the problem by installing "default-jre" and "gcj-jre". These two will install the other packages mentioned by blab_blab and rCX.

imageJ depencies include "giJ | java2-runtime". Java2-runtime should install the needed packages but it is not present in 9.10 repositories.

Java2-runtime is a "virtual package provided by default-jre, gcj-4.4-jre, gcj-jre, java-gcj-compat, openjdk-6-jre, sun-java6-jre" (I checked in the debian repositories).

[BobC (flymypg)]

Verified 1) problem still exists, and 2) fix recommended by Carnë Draug works.

[Charles Plessy (plessy)]

Hello everybody,

This is fixed in Lucid since version 1.43l-1, that depends on openjdk-6-jre | java2-runtime.

Have a nice day,

--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

[Thomas Ibbotson (thomas-ibbotson)]

As lucid is out now, I'm marking this as Fix Released.