[ImageJ-builds] Build failed in Jenkins: fiji-full #690

Jenkins Daemon jenkins at qa.nest-initiative.org
Mon Apr 1 14:45:58 CDT 2013 

See <https://qa.nest-initiative.org/job/fiji-full/690/>

------------------------------------------
[...truncated 114 lines...]
cast to java.lang.Object[] for a non-varargs call and to suppress this warning
				m.invoke(null, null);
				               ^
<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/src/main/java/MacClipboard.java>:127: warning: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Class for a varargs call
cast to java.lang.Class[] for a non-varargs call and to suppress this warning
			m = c.getMethod("getNaturalBounds", null);
			                                    ^
<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/src/main/java/MacClipboard.java>:128: warning: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Object for a varargs call
cast to java.lang.Object[] for a non-varargs call and to suppress this warning
			Object rect= m.invoke(importer, null);
			                                ^
<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/src/main/java/MacClipboard.java>:132: warning: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Class<?> for a varargs call
cast to java.lang.Class<?>[] for a non-varargs call and to suppress this warning
			m = rect.getClass().getMethod("getWidth", null);
			                                          ^
<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/src/main/java/MacClipboard.java>:133: warning: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Object for a varargs call
cast to java.lang.Object[] for a non-varargs call and to suppress this warning
			Integer width= (Integer)m.invoke(rect, null);
			                                       ^
<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/src/main/java/MacClipboard.java>:134: warning: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Class<?> for a varargs call
cast to java.lang.Class<?>[] for a non-varargs call and to suppress this warning
			m = rect.getClass().getMethod("getHeight", null);
			                                           ^
<https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA/src/main/java/MacClipboard.java>:135: warning: non-varargs call of varargs method with inexact argument type for last parameter;
cast to java.lang.Object for a varargs call
cast to java.lang.Object[] for a non-varargs call and to suppress this warning
			Integer height= (Integer)m.invoke(rect, null);
			                                        ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
10 warnings
Compiling 26 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/fiji-lib>
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 22 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/pal-optimization>
Compiling 190 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/VIB-lib>
Note: Some input files use or override a deprecated API.
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Note: Some input files use unchecked or unsafe operations.
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Compiling 251 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib1/core>
Compiling 121 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Viewer>
Note: Some input files use or override a deprecated API.
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Compiling 35 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/level_sets>
Note: Some input files use unchecked or unsafe operations.
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Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Blob_Segmentation>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Blob_Segmentation/src/main/java/ij3d/segmentation/Blob_Segmentation_in_3D.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Blob_Segmentation/src/main/java/ij3d/segmentation/Blob_Segmentation_in_3D.java> uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 4 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Objects_Counter>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/3D_Objects_Counter/src/main/java/Utilities/Counter3D.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 121 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/mpicbg/mpicbg>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/modules/mpicbg/mpicbg/src/main/java/mpicbg/ij/InteractiveInvertibleCoordinateTransform.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 87 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib1/algorithms>
Compiling 21 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib1/ij>
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 3 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Algorithm_Launcher>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Algorithm_Launcher/src/main/java/AlgorithmInfo.java> uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 6 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/AnalyzeSkeleton_>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/AnalyzeSkeleton_/src/main/java/skeleton_analysis/AnalyzeSkeleton_.java> uses unchecked or unsafe operations.
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Compiling 2 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Analyze_Reader_Writer>
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Anisotropic_Diffusion_2D>
Compiling 3 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Arrow_>
Compiling 2 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Auto_Threshold>
Compiling 8 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/BalloonSegmentation_>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/BalloonSegmentation_/src/main/java/BalloonSegmentation_.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
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Warning: <https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar> overrides com.sun>tools

Warning: <https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar> overrides com.sun>tools

Compiling 26 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/fiji-compat>
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
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Compiling 3 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/fiji-scripting>
Note: Some input files use unchecked or unsafe operations.
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Compiling 2 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/BeanShell_Interpreter>
Compiling 202 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2/core/core>
Note: imagej.module.DefaultModuleService indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.SaveInputsPreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.DebugPreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.LoadInputsPreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.DebugPostprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.InitPreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.ServicePreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.plugin.ValidityPreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.render.DummyRenderingService indexed under org.scijava.plugin.Plugin
Note: imagej.widget.DefaultWidgetService indexed under org.scijava.plugin.Plugin
Note: imagej.menu.DefaultMenuService indexed under org.scijava.plugin.Plugin
Note: imagej.display.ActiveDisplayPreprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.display.DisplayPostprocessor indexed under org.scijava.plugin.Plugin
Note: imagej.display.DefaultDisplayService indexed under org.scijava.plugin.Plugin
Note: imagej.display.DefaultTextDisplay indexed under org.scijava.plugin.Plugin
Note: imagej.platform.DefaultPlatformService indexed under org.scijava.plugin.Plugin
Note: imagej.platform.DummyAppService indexed under org.scijava.plugin.Plugin
Note: imagej.platform.DefaultPlatform indexed under org.scijava.plugin.Plugin
Note: imagej.command.DefaultCommandService indexed under org.scijava.plugin.Plugin
Note: imagej.options.DefaultOptionsService indexed under org.scijava.plugin.Plugin
Note: imagej.script.DefaultScriptService indexed under org.scijava.plugin.Plugin
Note: imagej.script.ScriptPlugin indexed under org.scijava.plugin.Plugin
Note: imagej.script.ScriptEngineList indexed under org.scijava.plugin.Plugin
Note: imagej.tool.DefaultToolService indexed under org.scijava.plugin.Plugin
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2/core/core/src/main/java/imagej/config/ConfigFileParameters.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 42 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2/core/updater>
Note: imagej.updater.ui.UpdatesAvailable indexed under org.scijava.plugin.Plugin
Note: imagej.updater.core.FileUploader indexed under org.scijava.plugin.Plugin
Note: imagej.updater.core.DefaultUploaderService indexed under org.scijava.plugin.Plugin
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2/core/updater/src/main/java/imagej/updater/util/Util.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 14 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2/ui/swing/updater>
Note: imagej.updater.gui.ImageJUpdater indexed under org.scijava.plugin.Plugin
Compiling 3 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Bug_Submitter>
Compiling 9 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/CLI_>
Note: Some input files use or override a deprecated API.
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Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/CPU_Meter>
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Calculator_Plus>
Compiling 2 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Clojure_Interpreter>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Clojure_Interpreter/src/main/java/Clojure/Clojure_Interpreter.java> uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 345 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib2/core>
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 59 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib2/algorithms/core>
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib2/algorithms/core/src/main/java/net/imglib2/algorithm/gauss/Gauss.java> uses unchecked or unsafe operations.
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Compiling 15 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib2/ij>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib2/ij/src/main/java/net/imglib2/img/display/imagej/ImageJVirtualStack.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 42 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Colocalisation_Analysis>
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Colocalisation_Analysis/src/main/java/results/SingleWindowDisplay.java> uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Color_Histogram>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Color_Histogram/src/main/java/ColorHistogram_.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 4 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Color_Inspector_3D>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Color_Inspector_3D/src/main/java/Color_Inspector_3D.java> uses or overrides a deprecated API.
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Compiling 1 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Colour_Deconvolution>
Compiling 8 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/CorrectBleach_>
Compiling 33 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Fiji_Plugins>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/Fiji_Plugins/src/main/java/Retinex_.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
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Compiling 16 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/SPIM_Opener>
Note: <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/SPIM_Opener/src/main/java/spimopener/GaussianStackFocuser.java> uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 2 files in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib/imglib1/io>
Compiling 146 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/SPIM_Registration>
<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/LRFFT.java>:164: cannot find symbol
symbol  : method setImageOutOfBoundsStrategy(mpicbg.imglib.outofbounds.OutOfBoundsStrategyValueFactory<mpicbg.imglib.type.numeric.real.FloatType>)
location: class mpicbg.imglib.algorithm.fft.FourierConvolution<mpicbg.imglib.type.numeric.real.FloatType,mpicbg.imglib.type.numeric.real.FloatType>
					conv.setImageOutOfBoundsStrategy( new OutOfBoundsStrategyValueFactory<FloatType>() );
					    ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 error
Exception in thread "main" imagej.build.minimaven.JavaCompiler$CompileError: Compile error: 1
	at imagej.build.minimaven.JavaCompiler.call(JavaCompiler.java:84)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:443)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:374)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:397)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:331)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:288)
	at imagej.build.MiniMaven.main(MiniMaven.java:133)
Warning: groupId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA's> parent: sc.fiji != com.github.scijava
Warning: artifactId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA's> parent: pom-fiji-submodules != pom-scijava
Warning: version mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/ImageJA's> parent: 2.0.0-SNAPSHOT != 1.4
Warning: groupId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/TrakEM2's> parent: sc.fiji != org.scijava
Warning: artifactId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/TrakEM2's> parent: pom-fiji-submodules != pom-scijava
Warning: version mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/TrakEM2's> parent: 2.0.0-SNAPSHOT != 1.24
Warning: groupId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2's> parent: sc.fiji != org.scijava
Warning: artifactId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2's> parent: pom-fiji-submodules != pom-scijava
Warning: version mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imagej2's> parent: 2.0.0-SNAPSHOT != 1.28
Warning: groupId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib's> parent: sc.fiji != org.scijava
Warning: artifactId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib's> parent: pom-fiji-submodules != pom-scijava
Warning: version mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/imglib's> parent: 2.0.0-SNAPSHOT != 1.13
Warning: groupId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/mpicbg's> parent: sc.fiji != org.scijava
Warning: artifactId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/mpicbg's> parent: pom-fiji-submodules != pom-scijava
Warning: version mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/mpicbg's> parent: 2.0.0-SNAPSHOT != 1.17
Warning: groupId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/scijava-common's> parent: sc.fiji != org.scijava
Warning: artifactId mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/scijava-common's> parent: pom-fiji-submodules != pom-scijava
Warning: version mismatch in <https://qa.nest-initiative.org/job/fiji-full/ws/modules/scijava-common's> parent: 2.0.0-SNAPSHOT != 1.28
Looking at children of pom-fiji
Looking at children of pom-fiji-plugins
Warning: <https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar> overrides com.sun>tools

Warning: <https://qa.nest-initiative.org/job/fiji-full/ws/java/linux/jdk1.6.0_24/jre/../lib/tools.jar> overrides com.sun>tools

Compiling 146 files in <https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/SPIM_Registration>
<https://qa.nest-initiative.org/job/fiji-full/ws/src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/LRFFT.java>:164: cannot find symbol
symbol  : method setImageOutOfBoundsStrategy(mpicbg.imglib.outofbounds.OutOfBoundsStrategyValueFactory<mpicbg.imglib.type.numeric.real.FloatType>)
location: class mpicbg.imglib.algorithm.fft.FourierConvolution<mpicbg.imglib.type.numeric.real.FloatType,mpicbg.imglib.type.numeric.real.FloatType>
					conv.setImageOutOfBoundsStrategy( new OutOfBoundsStrategyValueFactory<FloatType>() );
					    ^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 error
Exception in thread "main" imagej.build.minimaven.JavaCompiler$CompileError: Compile error: 1
	at imagej.build.minimaven.JavaCompiler.call(JavaCompiler.java:84)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:443)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:374)
	at imagej.build.minimaven.MavenProject.build(MavenProject.java:397)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:331)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:326)
	at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:288)
	at imagej.build.MiniMaven.main(MiniMaven.java:133)
Build step 'Execute shell' marked build as failure

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