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  • Dec 09 15:10

    tinevez on jungle

    Avoid keyboard clashes with BDV… Merge remote-tracking branch 'o… (compare)

  • Dec 09 14:48
    tinevez synchronize #85
  • Dec 09 14:48

    tinevez on harness-2d

    Avoid keyboard clashes with BDV… (compare)

  • Dec 09 13:30

    tinevez on jungle

    Harness 2D datasets in BDV view… Merge remote-tracking branch 'o… (compare)

  • Dec 03 12:17
    tinevez commented #90
  • Nov 28 03:30
    ctrueden commented #90
  • Nov 28 03:29
    ctrueden synchronize #90
  • Nov 27 07:59
    tinevez commented #90
  • Nov 22 09:28
    tinevez commented #90
  • Nov 22 09:26
    imagejan commented #90
  • Nov 22 09:00

    tinevez on master

    Utility to select text color ba… Select text color in the colorm… (compare)

  • Nov 22 08:40
    tinevez commented #90
  • Nov 21 20:22
    tinevez closed #133
  • Nov 21 20:22
    tinevez commented #133
  • Nov 21 18:16
    jeffreyEdgarYeung commented #133
  • Nov 21 17:04
    imagejan commented #90
  • Nov 21 17:01
    imagejan commented #90
  • Nov 21 16:24
    tinevez closed #83
  • Nov 21 16:24
    tinevez commented #83
  • Nov 21 16:24
    tinevez opened #110
Varun Kapoor
@kapoorlab
@imagejan Thanks :) no wildcards, ok am getting an error which I do not understand:
Failure to transfer sc.fiji:TrackMate_:jar:3.6.1 from http://maven.imagej.net/content/groups/public was cached in the local repository, resolution will not be reattempted until the update interval of imagej.public has elapsed or updates are forced.
tpietzsch
@tpietzsch
That means maven tried to download sc.fiji:TrackMate_:jar:3.6.1 and failed for some reason
It will not reattempt to download for some period of time
instead remember that this failed
you can force it retry by running with -U option
(e.g. mvn clean package -U)
@kapoorlab
Varun Kapoor
@kapoorlab
@tpietzsch yeah it is the reason thats bugging me, i will try force, clean with/without wifi/ethernet. Thanks Tobias
Curtis Rueden
@ctrueden
@kapoorlab If you still have trouble, you can also rm -rf ~/.m2/repository/sc/fiji/TrackMate_. This is sometimes necessary if a JAR file is corrupted during download.
amirffff
@amirffff
HI can I ask a question the manager of this Chat?
Niko Ehrenfeuchter
@ehrenfeu
@amirffff this is an open community, you can ask your question right here.
Varun Kapoor
@kapoorlab
@ctrueden Thanks Curtis, I got it working. About the 3D displayer, is it out already? When I try to use it I get: java.lang.NoClassDefFoundError: org/scijava/java3d/utils/universe/SimpleUniverse, Is hyperstack viewer the only other option left?
odinsbane
@odinsbane
Is there a way for providing an incremental update without updating an update site?
Jan Eglinger
@imagejan
@kapoorlab the class org.scijava.java3d.utils.universe.SimpleUniverse is in the org.scijava.j3dutils artifact: http://maven.imagej.net/#nexus-search;classname~org.scijava.java3d.utils.universe.SimpleUniverse
AFAICT, this is related to the 'old' 3D Viewer, and not SciView (if this is what you meant with "3D displayer"). SciView can be used via separate update site.
Jan Eglinger
@imagejan
@odinsbane what do you mean by incremental update? There's currently no possibility to define "inter-dependencies" between update sites. You can also point people to jar files built automatically by Travis and uploaded to the maven repository.
(If it's just for testing etc)
Why not uploading to the existing update site?
odinsbane
@odinsbane
I am doing some work with the plugin, so I might have more updates in the near future. Ill probably just upload to the existing site though.
I don't really have a good reason not to. It is just a pretty small change.
Varun Kapoor
@kapoorlab
@imagejan Thanks, I did that and now I get a new error: java.util.concurrent.ExecutionException: java.lang.UnsatisfiedLinkError: Can't load library: /Users/aimachine/PreProcessingSuite/natives/macosx-universal//gluegen-rt
There is no directory called natives in my PreProcessingSuite folder
Varun Kapoor
@kapoorlab
Maybe I will just try SciView
Varun Kapoor
@kapoorlab
@tinevez Same error in Trackmate when I try to run it from Eclipse as a cloned repo (execture TrackMatePLugin_.java): Exception in thread "TrackMate view rendering thread" java.lang.UnsatisfiedLinkError: Can't load library: /Users/aimachine/TrackMate/natives/macosx-universal//gluegen-rt
odinsbane
@odinsbane
@kapoorlab they should be in a jar file something along the line of gluegen-natives-rt or some such thing.
I don't know why, but for working with Intellij I had to unpack the jarfiles and then add the libraries to the java.library.path when I run programs with java3d.
Varun Kapoor
@kapoorlab
@odinsbane where did you get those jar files from?
odinsbane
@odinsbane
The all platforms will have everything, including other platforms. I just use the natives-macosx-universal.jar (s) Four of them.
On linux the native jar files load fine, but on osx, for some reason I had to unpack them. Although I think fiji/3d viewer works out of the box for me.
Varun Kapoor
@kapoorlab
The file has an extension of 7z, how do you unpack such a file?
odinsbane
@odinsbane
There is a program 7zip.
@kapoorlab Do you have a version of fiji working with the 3D viewer? If so it will have the jar files you need.
Varun Kapoor
@kapoorlab
Ah let me check
odinsbane
@odinsbane
When I go into the Fiji.app folder, they're under jars/macosx/ Then there are four of them.
Varun Kapoor
@kapoorlab
Oh yeah the 3D viewer works in Fiji, just not on eclipse
odinsbane
@odinsbane
I spent a little time trying to get Intellij to work with the native jar files and not unpack them, but I just ended up unpacking them and it worked.
Varun Kapoor
@kapoorlab
I c, so I have to point these jars on the java build path for the repo I want to use the 3D viewer in, right?
odinsbane
@odinsbane
The only way I could get it to work was to unpack the jarfiles and then when I run the program include an argument to the jvm. -Djava.library.path=/path/to/folder/with/jnilibs
Hopefully somebody chimes in with the correct way to do this. I would much prefer to just include the jarfiles.
Varun Kapoor
@kapoorlab
No it works that way, I just did this to trackmate in eclipse: Right click on repo, -> Build Path -> Add external Archives -> Then add all the four jars in the Fiji macos folder that you mentioned and then it works
Curtis Rueden
@ctrueden
@odinsbane It should not be necessary to manually unpack natives from JARs in IntelliJ. The Java code is supposed to provide magic to take care of that for you. Maybe @skalarproduktraum has some insight?
Jean-Yves Tinevez
@tinevez
Hi all.
I am having troubles creating a new update site for Fiji.
I successfully created the TrackMateCSVImporteraccount on the wiki, and validated my email. But when I try to create the corresponding update site in Fiji updater, it does not work.
I cliked on Add my site in the updater, and input TrackMateCSVImporter as account name. The updater then asks me for my password, but it rejects it and this message appears in the console:
Did not get a token!
Did I do something wrong?
Jan Eglinger
@imagejan
You did set the upload password in addition to your wiki password, right?
Jean-Yves Tinevez
@tinevez

And another question: (sorry for the spam).
I meet a enforcer-related compile error for this very project.
It depends on the bioformats_plugin artifact, and it generate the following error:

[WARNING] Rule 3: org.apache.maven.plugins.enforcer.BanDuplicateClasses failed with message:
No Duplicate Classes Allowed!
- For duplicate transitive dependencies, add dependency exclusions.
- For duplications between direct dependencies, resolve or add
  ignored classes to this rule's configuration.

  Found in:
    commons-io:commons-io:jar:2.6:compile
    ch.systems.cisd:jhdf5:jar:14.12.0:compile
  Duplicate classes:
    org/apache/commons/io/FileCleaningTracker.class
    org/apache/commons/io/comparator/SizeFileComparator.class
    org/apache/commons/io/output/ProxyWriter.class

which is fine I guess. But how to skip this?

@imagejan .... no
Where do you do this?