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Bug 963 - Error Opening and Building Fiji with TrakEM2
Error Opening and Building Fiji with TrakEM2
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: TrakEM2
unspecified
PC Windows
: P5 critical
Assigned To: Albert Cardona
Depends on:
Blocks:
 
Reported: 2014-11-25 11:03 CST by Eric Budiman Gosno
Modified: 2015-02-27 10:29 CST
2 users (show)

See Also:
Description Eric Budiman Gosno 2014-11-25 11:03:30 CST 
I am currently conduct several researches regarding Image Registration Alignment by using Fiji with TrakEM2 Framework which I need to add and modify several codes inside TrakEM2 (I used Fiji  1.49j10 with pom-fiji 2.0.0-SNAPSHOT and TrakEM2 1.0a)

Until last Thursday(November 20, 2014), I still could build Fiji and TrakEM2 perfectly by using command "./Build.sh" or "sh Build.sh run", but in the last friday(November 21), I found an error regarding null:scijava-common(as shown below) when I tried to build fiji and TrakEM2 

Looking at children of pom-fiji
Exception in thread "main" java.lang.IllegalArgumentException: Need fully qualified GAVs: null:scijava-common:2.35.1
	at imagej.build.minimaven.MavenProject.findPOM(MavenProject.java:998)
	at imagej.build.minimaven.MavenProject.getDependencies(MavenProject.java:760)
	at imagej.build.minimaven.MavenProject.getDependencies(MavenProject.java:791)
	at imagej.build.minimaven.MavenProject.getDependencies(MavenProject.java:791)
	at imagej.build.minimaven.MavenProject.getDependencies(MavenProject.java:791)
	at imagej.build.minimaven.MavenProject.getDependencies(MavenProject.java:743)
	at imagej.build.minimaven.MavenProject.checkUpToDate(MavenProject.java:209)
	at imagej.build.minimaven.MavenProject.upToDate(MavenProject.java:194)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:404)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:346)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:341)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:302)
	at imagej.build.MiniMaven.main(MiniMaven.java:144)

I already tried to clone new Fiji source, but the new fiji is not recognizing the TrakEM2 module as there is no "New TrakEM2(Blank)" Menu and if I tried to open the TrakEM2 xml, there will be error as shown below

(Fiji Is Just) ImageJ 2.0.0-rc-17/1.49j10; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 27MB of 12235MB (<1%)
 
java.io.IOException: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: QuickTime resource fork not found.  To avoid this issue, please flatten your QuickTime movies before importing with SCIFIO.

	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:140)

	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:109)

	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:63)

	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)

	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)

	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)

	at ij.IJ.runPlugIn(IJ.java)

	at ij.Executer.runCommand(Executer.java:131)

	at ij.Executer.run(Executer.java:64)

	at java.lang.Thread.run(Thread.java:662)

Caused by: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: QuickTime resource fork not found.  To avoid this issue, please flatten your QuickTime movies before importing with SCIFIO.

	at io.scif.img.ImgOpener.createReader(ImgOpener.java:551)

	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)

	at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:133)

	... 9 more

Caused by: java.io.IOException: io.scif.FormatException: QuickTime resource fork not found.  To avoid this issue, please flatten your QuickTime movies before importing with SCIFIO.

	at io.scif.AbstractReader.setSource(AbstractReader.java:274)

	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)

	at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)

	... 11 more

Caused by: io.scif.FormatException: QuickTime resource fork not found.  To avoid this issue, please flatten your QuickTime movies before importing with SCIFIO.

	at io.scif.formats.qt.NativeQTFormat$Parser.typedParse(NativeQTFormat.java:445)

	at io.scif.formats.qt.NativeQTFormat$Parser.typedParse(NativeQTFormat.java:353)

	at io.scif.AbstractParser.parse(AbstractParser.java:252)

	at io.scif.AbstractParser.parse(AbstractParser.java:335)

	at io.scif.AbstractParser.parse(AbstractParser.java:52)

	at io.scif.AbstractReader.setSource(AbstractReader.java:270)

	... 13 more



  os.arch => x64
  os.name => Windows 7
  os.version => 7.0
  java.version => 1.7.0_51
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_51-b13
  java.vm.name => Java HotSpot(TM) 64-bit server VM
  java.vm.version => 24.51-b03
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  sun.desktop => windows
  file.separator => \
Comment 1 Mark Hiner 2015-02-27 10:29:34 CST 
Hi Eric,

Sorry to hear Build.sh is broken for you. Please note that the Build.sh script is not the recommended way to build Fiji from source; you may have better luck with Maven[1]. 

Also, in January we restructured how TrakEM2 is used by Fiji in a move towards a fully reproducible Fiji[2], so I am curious if you are still having this problem?

Finally, it is unfortunate that you have to modify TrakEM2 files manually. I doubt that it's affecting the build system, but if you're forking the code it can make troubleshooting more difficult. You may instead want to submit a pull request to get your changes back to the TrakEM2 source[3].

[1] http://imagej.net/Downloading_and_Building_Fiji_From_Source

[2] https://github.com/fiji/fiji/commit/04f283aa19ce8fe75d6c8a2605e8454bdda59e2d

[3] https://github.com/trakem2/trakem2