Bug#732222: fiji acted - was:Re: Bug#732222: imagej: does not see present JAVA

2013-12-16 Thread Martin Weiser 
Andreas Tille píše v Po 16. 12. 2013 v 15:07 +0100:
 Hi Martin,
 
 On Mon, Dec 16, 2013 at 02:04:34PM +0100, Martin Weiser wrote:
  Sorry. I hope I get it know:
  
  louskacek@zouzel:~$ ./imagej.sh
  + ./imagej.sh
  + set +u
  + shopt -s extglob
  + '[' -z /usr/lib/jvm/java-1.7.0-openjdk-i386 ']'
  + ij_path=/usr/share/java
  + ij_user_path=/home/louskacek/.imagej
  + ijadmin=debian-med-packag...@lists.alioth.debian.org
  + doc_url=http://imagej.nih.gov/ij/
  + ij_tmp=/home/louskacek/.imagej/tmp
  + newwindow=true
  + separator=:
  + declare -i mem
  + declare -i default_mem=500
  + declare -i min_mem=16
  + declare -i max_mem
  + declare -i free_mem
  ++ pwd
  + dir=/home/louskacek
  ++ whoami
  + user=louskacek
  ++ hostname
  + host=zouzel
  + [[ -z :0 ]]
  + display=:0
  + declare -i port=0
  + declare -i verbosity=0
  + images=
  + macrocmd=
  + macroargs=
  ++ uname
  + [[ Linux == \S\u\n\O\S ]]
  ++ uname
  + [[ Linux == \L\i\n\u\x ]]
  ++ uname -m
  + [[ i686 == \x\8\6\_\6\4 ]]
  + arch=-d32
  + java_path=/usr/share/java/jre/bin/java
  ++ free
  ++ awk 'NR == 2 {fmem=int($2 / 1024); if (fmem  1800) {print fmem} else
  {print 1800}}'
  + max_mem=1800
  ++ free
  ++ awk 'NR == 3 {fmem=int($4 / 1024); if (fmem  1800) {print fmem} else
  {print 1800}}'
  + free_mem=1800
  + mem='1800/3*2'
  + ((  1200  500 || 1200  16  ))
  + mem=500
  + mkdir -p /home/louskacek/.imagej/plugins
  + mkdir -p /home/louskacek/.imagej/macros
  + mkdir -p /home/louskacek/.imagej/luts
  + [[ ! -d /home/louskacek/.imagej/tmp ]]
  + ls /usr/share/imagej/plugins
  + read p
  + '[' '!' -e /home/louskacek/.imagej/plugins/JavaScriptEvaluator.class
  ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/plugins/MacAdapter.class ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/plugins/MacClipboard.class ']'
  + read p
  + read p
  + ls /usr/share/imagej/macros
  + '[' '!' -e /home/louskacek/.imagej/macros/AddParticles.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/ConvertStackToBinary.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/EnlargeSelection.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/HyperStackMaker.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/MoveSelection.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/RotateSelection.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/Search.txt ']'
  + read p
  + '[' '!' -e '/home/louskacek/.imagej/macros/Stack Tools.txt' ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/StartupMacros.txt ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/macros/TimeStamp.ijm ']'
  + read p
  + ls /usr/share/imagej/luts
  + read p
  + '[' '!' -e /home/louskacek/.imagej/luts/HiLo.lut.enc ']'
  + read p
  + '[' '!' -e /home/louskacek/.imagej/luts/RedHot.lut.enc ']'
  + read p
  + modules='-cp /usr/share/java/ij.jar'
  + tools=/usr/lib/jvm/java-1.7.0-openjdk-i386/lib/tools.jar
  + getopts b:ce:hi:m:op:r:vx: options
  + declare -i i=1
  + ((  i  1  ))
  + [[ -n '' ]]
  + ((  0  0  ))
  + pushd /home/louskacek/.imagej/tmp
  + declare -i count=1
  + portopen=false
  + lockFileCreated=false
  + locklist=(`ls | grep '[0-9][0-9]-.*'`)
  ++ grep '[0-9][0-9]-.*'
  ++ ls
  + declare -a locklist
  + ((  0  0  ))
  + ((  0  0  ))
  + [[ true == \f\a\l\s\e ]]
  + [[ false == \f\a\l\s\e ]]
  + ((  0 == 0  ))
  + ((  0 == 0  ))
  + count=1
  ++ printf %02u 1
  + prefix=01
  + lockname=01-louskacek-zouzel-:0
  + ((  0  0  ))
  + touch 01-louskacek-zouzel-:0
  + trap '\rm -f ${ij_tmp}/$lockname /dev/null ; exit 1' EXIT TERM
  + ((  0  0  ))
  + lockFileCreated=true
  + echo 'Open other images in this ImageJ panel as follows:'
  Open other images in this ImageJ panel as follows:
  + echo '  imagej -p 1 image1 [image2 ... imageN]'
imagej -p 1 image1 [image2 ... imageN]
  + ((  0  0  ))
  + echo
  
  + popd
  + '[' -d /usr/share/imagej/jni/ ']'
  + '[' /usr/lib/jvm/java-1.7.0-openjdk-i386 ']'
  + ((  0  0  ))
  + eval /usr/lib/jvm/java-1.7.0-openjdk-i386/bin/java -d32 -mx500m
  -cp /usr/share/java/ij.jar ij.ImageJ -ijpath /home/louskacek/.imagej
  -port1
  ++ /usr/lib/jvm/java-1.7.0-openjdk-i386/bin/java -d32 -mx500m
  -cp /usr/share/java/ij.jar ij.ImageJ -ijpath /home/louskacek/.imagej
  -port1
  Exception in thread main java.awt.HeadlessException
  at
  java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
  at java.awt.Window.init(Window.java:535)
  at java.awt.Frame.init(Frame.java:420)
  at ij.ImageJ.init(ImageJ.java:129)
  at ij.ImageJ.main(ImageJ.java:597)
  + exit 0
  + rm -f /home/louskacek/.imagej/tmp/01-louskacek-zouzel-:0
  + exit 1
  louskacek@zouzel:~$ 
  
  Is this OK?
 
 This is what we wanted to know and it seems you are running this on a i386
 system.  I tested the resulting call on my amd64 system by
 
 
 /usr/lib/jvm/java-1.7.0-openjdk-amd64/bin/java -d64 -mx500m -cp 
 /usr/share/java/ij.jar ij.ImageJ -ijpath /home/tillea/.imagej -port1

Bug#732222: fiji acted - was:Re: Bug#732222: imagej: does not see present JAVA

2013-12-16 Thread Andreas Tille 
Hi Martin,

On Mon, Dec 16, 2013 at 04:30:39PM +0100, Martin Weiser wrote:
 problem solved. Probably there was some interference in setting
 environment variables between Imagej and Fiji.
 
 I purged Fiji, ImageJ, Java, 
 then re-installed ImageJ:
 ImageJ worked 
 
 When I added Fiji, ImageJ stopped to work with the originally
 bug-reported quote.
 
 When I purged Fiji, ImageJ still did not work.
 
 I purged Imagej and Java again, and then re-installed Imagej.
 ImageJ works.

Thanks for tracking down what we had no chance for!

 Maybe it is openjdk/gcj java problem:
 
 Simple removal of ImageJ did not helped, as installing Fiji leads to
 installing gcj-java. When there were both these Javas (gcj and openjdk),
 ImageJ refuted to work. 
 
 It seems to me that maybe the problem is that ImageJ tries to work with
 openjdk Java, while it should work with gcj? Or anything else? (Or maybe
 even better: Fiji should not depend on another Java?)

I have no idea from where you are installing Fiji since there are no
official Debian packages of it.  While we considered this in the past
people who know more about internals of Fiji considered this a bad idea
(there should be some record at the Debian Med list about this
discussion).  In any case it seems to be a bad idea to not depend from
openjdk if you want to run on a recent Debian system.  Those inofficial
Fije packages should be fixed ... or even better the maintainers should
cooperate with us instead of making trouble to their users.

 Thank you for your interest and help.

Thanks for your report in any case.  Please let us know about your ideas
about Fiji maintained in Debian.

Kind regards

  Andreas.

-- 
http://fam-tille.de


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