StartupMacros not loading on Linux system

[axm2]

I have a strange behaviour on Linux

If I execute imageJ from its normal working path, the startupMacros are not
loaded (my own compile). If I run the same imageJ from within JBuilder2006,
then the startup macros are loaded as expected. The macros also load
perfectly normal with the SAME compiled imageJ if I run it on a Windows PC.

Given that the problem does not occur from within JBuilder, this is a bit
tricky to debug, however, I dug down with a lot of System.out.println
commands to narrow the problem down.

in Menus.java, version 1.41h line 782 macrosPath is defined correctly:
  macrosPath = pluginsDir+Prefs.separator+"macros"+Prefs.separator;

//but then
  macrosPath = pluginsDir+Prefs.separator+"macros"+Prefs.separator;
}
File f = macrosPath!=null?new File(macrosPath):null;
  if (f!=null && !f.isDirectory())
    macrosPath = null;

macrosPath is set to null on Linux if and only if run from a console due to
f.isDirectory()
returning an incorrect value.

I ruled out that this is a file permission problem by double-checking
permissions and repeating the test as a superuser. I am appending some log
messages I got from additional System.out.println statements when running
ImageJ as either from a superuser shell (macros failing to load) or from
within JBuilder (working as expected and as on a Windows system).

System:
imageJ version 1.39s (but should also happen in 1.41h from a quick look at
the code)
SUSE 10.3 x64, jdk1.6.0_04, JBuilder2006, reproducible on SUSE 11 x64 with
jdk1.6.0_08

Any ideas or workarounds most welcome!
Tux

////////// failed to load from shell ////////////////////////
11:48 tux:../ij/ij-139s-am129 > su
Password:
11:48 tux:../ij/ij-139s-am129 # ./ij-dev-run-laptop
homeDir==null
homeDir (b)=/home/arndt/j/ij/ij-139s-am129
homeDir (c)=/home/arndt/j/ij/ij-139s-am129
userHome (a)=/root
prefsDir (b)=/root/.imagej
FileInputStream(homeDir+/+PROPS_NAME),
arg=/home/arndt/j/ij/ij-139s-am129/IJ_Props.txt
loadPreferences(path) path=/root/.imagej/IJ_Prefs.txt
homeDir=/home/arndt/j/ij/ij-139s-am129
pluginsPath (b)=null
pluginsPath (d)=/home/arndt/j/ij/ij-139s-am129/plugins/plugins/
macrosPath (a)=/home/arndt/j/ij/ij-139s-am129/plugins/macros/
(macrosPath != null) with
macrosPath=/home/arndt/j/ij/ij-139s-am129/plugins/macros/
f.getPath()= /home/arndt/j/ij/ij-139s-am129/plugins/macros
f.getName()= macros
f.exists() is false for /home/arndt/j/ij/ij-139s-am129/plugins/macros
f.isDirectory() is false for /home/arndt/j/ij/ij-139s-am129/plugins/macros
f.isFile() is false for /home/arndt/j/ij/ij-139s-am129/plugins/macros
f.Absolute is true for /home/arndt/j/ij/ij-139s-am129/plugins/macros
f.canWrite() is false for /home/arndt/j/ij/ij-139s-am129/plugins/macros
f.pathSeparator= :
f.separator= /
macrosPath (b)=/home/arndt/j/ij/ij-139s-am129/plugins/macros/


///////////// same log when run from JBuilder - good behaviour ///////
/usr/java/jdk1.6.0_04/bin/java -classpath
"/home/arndt/j/ij/ij-139s-am129/plugins:/usr/java/jdk1 [..]
/jnlp-servlet.jar"  -mx764m ij.ImageJ
homeDir==null
homeDir (b)=/home/arndt/j/ij/ij-139s-am129
homeDir (c)=/home/arndt/j/ij/ij-139s-am129
userHome (a)=/home/arndt
prefsDir (b)=/home/arndt/.imagej
FileInputStream(homeDir+/+PROPS_NAME),
arg=/home/arndt/j/ij/ij-139s-am129/IJ_Props.txt
loadPreferences(path) path=/home/arndt/.imagej/IJ_Prefs.txt
homeDir=/home/arndt/j/ij/ij-139s-am129
pluginsPath (b)=null
pluginsPath (d)=/home/arndt/j/ij/ij-139s-am129/plugins/
macrosPath (a)=/home/arndt/j/ij/ij-139s-am129/macros/
(macrosPath != null) with macrosPath=/home/arndt/j/ij/ij-139s-am129/macros/
f.getPath()= /home/arndt/j/ij/ij-139s-am129/macros
f.getName()= macros
f.exists() is true for /home/arndt/j/ij/ij-139s-am129/macros
f.isDirectory() is true for /home/arndt/j/ij/ij-139s-am129/macros
f.isFile() is false for /home/arndt/j/ij/ij-139s-am129/macros
f.Absolute is true for /home/arndt/j/ij/ij-139s-am129/macros
f.canWrite() is true for /home/arndt/j/ij/ij-139s-am129/macros
f.pathSeparator= :
f.separator= /
macrosPath (b)=/home/arndt/j/ij/ij-139s-am129/macros/

[dscho]

Hi Tux,

On Tue, 22 Jul 2008, Tux Hacker wrote:


> ////////// failed to load from shell ////////////////////////
> 11:48 tux:../ij/ij-139s-am129 > su
> Password:

What the... ? Running ImageJ as _root_?

> pluginsPath (b)=null
> pluginsPath (d)=/home/arndt/j/ij/ij-139s-am129/plugins/plugins/

This tells me that your script to run ImageJ from the command line sets
plugins.dir to .../plugins/!  Compare that to theoutput from JBuilder:

> ///////////// same log when run from JBuilder - good behaviour ///////
>
> [...]
> userHome (a)=/home/arndt

Saner.

> pluginsPath (b)=null
> pluginsPath (d)=/home/arndt/j/ij/ij-139s-am129/plugins/

It obviously sets plugins.dir _not_ to .../plugins/.

Hth,
Dscho