[Debian-med-packaging] Bug#732222: fiji acted - was:Re: Bug#732222: imagej: does not "see" present JAVA

[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 at 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-packaging at 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 at 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
> 
> 
> and it works perfectly.  I admit that I'm a bit lost now since I do not
> have a clue what might be wrong at your side.  Anybody else who might
> be able to reproduce this?
> 
> Kind regards
> 
>        Andreas.
> 
Hi Andreas,

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.

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?)

Thank you for your interest and help.
Best,
Martin 

This is the output of the script again (ImageJ works):

louskacek at zouzel:~$ ./imagej.sh
+ set +u
+ shopt -s extglob
+ '[' -z '' ']'
++ /usr/sbin/update-java-alternatives -l
++ tail -1
++ grep openjdk
++ cut '-d ' -f 3
++ sort
+ JAVA_HOME=/usr/lib/jvm/java-1.6.0-openjdk-i386
+ ij_path=/usr/share/java
+ ij_user_path=/home/louskacek/.imagej
+ ijadmin=debian-med-packaging at 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 ]]
+ read p
+ ls /usr/share/imagej/plugins
+ '[' '!' -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-1.6.0-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-1.6.0-openjdk-i386 ']'
+ ((  0 > 0  ))
+ eval /usr/lib/jvm/java-1.6.0-openjdk-i386/bin/java -d32 -mx500m
-cp /usr/share/java/ij.jar ij.ImageJ -ijpath /home/louskacek/.imagej
-port1
++ /usr/lib/jvm/java-1.6.0-openjdk-i386/bin/java -d32 -mx500m
-cp /usr/share/java/ij.jar ij.ImageJ -ijpath /home/louskacek/.imagej
-port1
+ exit 0
+ rm -f /home/louskacek/.imagej/tmp/01-louskacek-zouzel-:0
+ exit 1