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Bug 623 - Fiji Build fails on VIB_
Fiji Build fails on VIB_
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-06-19 09:52 CDT by Stephan Preibisch
Modified: 2013-06-19 11:13 CDT
2 users (show)

See Also:

Description Stephan Preibisch 2013-06-19 09:52:28 CDT
Did a clean builld, update, clean build ... doesn't change. That sounds like something is wrong with the Maven dependencies? The "^" points at the dot in triangulator.getTriangles ...

Compiling 117 files in /groups/myers/home/preibischs/fiji/src-plugins/VIB_
/groups/myers/home/preibischs/fiji/src-plugins/VIB_/src/main/java/marchingcubes/ExportMesh_.java:35: cannot access mpicbg.imglib.type.numeric.RealType
class file for mpicbg.imglib.type.numeric.RealType not found
		List mesh = triangulator.getTriangles(
		                        ^

Thanks a lot for any help,
Steffi

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.32-279.el6.x86_64
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /groups/myers/home/preibischs/fiji/java/linux-amd64/jdk1.6.0_24//jre
  ij.dir => /groups/myers/home/preibischs/fiji

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2013-06-19 10:19:53 CDT
Do you have the TrakEM2 module checked out? For the moment, we had to commit a new revision of said module into fiji.git which is not yet available on repo.or.cz (but I sent a pull request).

So: if ''git submodule update modules/TrakEM2'' fails in your Fiji checkout with an error message suggesting that it did not find a particular TrakEM2 commit or tree, execute these commands in the root directory of your Fiji checkout:

(cd modules/TrakEM2 &&
 git remote add -f fiji https://github.com/fiji/TrakEM2) &&
git submodule update modules/TrakEM2
Comment 2 Stephan Preibisch 2013-06-19 10:31:33 CDT
Hi Johannes,

no, the TrakEM2 submodule is not checked out. But if this might clear out later anyways do not bother now with it now. I got the SPIM deconvolution compiling and running without it for now although the build fails.

Thanks a lot, Steffi
Comment 3 Johannes Schindelin 2013-06-19 10:57:42 CDT
Oops, you're correct: I forgot to update the Jenkins job deploying TrakEM2. Fixed now: http://jenkins.imagej.net/job/TrakEM2-Maven/29/console
Comment 4 Stephan Preibisch 2013-06-19 11:13:53 CDT
Thanks Johannes!