[ImageJ-builds] Build failed in Jenkins: Fiji-minimal #679

jenkins at imagej.net jenkins at imagej.net
Thu Jul 12 11:37:26 CDT 2012 

See <http://jenkins.imagej.net/job/Fiji-minimal/679/>

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[...truncated 216 lines...]
Building jars/mpicbg.jar <- jars/ij.jar jars/Jama.jar modules/mpicbg/
Building plugins/Fiji_Updater.jar <- src-plugins/Fiji_Updater/
Compiling 48 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Updater
Building jars/mpicbg.jar <- plugins/Fiji_Updater.jar jars/ij.jar j...
Updating the Fiji database (Updating from Fiji site) 
Updating the Fiji database 0/1

(process:24320): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
GConf Error: No D-BUS daemon running


(process:24320): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
GConf Error: No D-BUS daemon running

Updating from Fiji site done
Done: Updating the Fiji database

Czech Summer (jars/Jama.jar) 
jars/Jama.jar done
Czech Summer 33050/2837562
Czech Summer (jars/ij.jar) 
jars/ij.jar done
Czech Summer (jars/javac.jar) 
jars/javac.jar done
Czech Summer (jars/mpicbg.jar) 
jars/mpicbg.jar done
Done: Czech Summer

Skipping locally-modified jars/Jama.jar
Skipping locally-modified jars/ij.jar
Skipping locally-modified jars/javac.jar

(process:24320): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
GConf Error: No D-BUS daemon running

Downloading... (jars/mpicbg.jar) 
Downloading... 89949/248483
jars/mpicbg.jar done
Done: Downloading...

Installed jars/mpicbg.jar
Building plugins/mpicbg_.jar <- jars/ij.jar jars/mpicbg.jar module...
Building plugins/mpicbg_.jar <- plugins/Fiji_Updater.jar jars/ij.j...
Updating the Fiji database (Updating from Fiji site) 
Updating the Fiji database 0/1

(process:24381): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
GConf Error: No D-BUS daemon running


(process:24381): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
GConf Error: No D-BUS daemon running

Updating from Fiji site done
Done: Updating the Fiji database

Czech Summer (jars/ij.jar) 
jars/ij.jar done
Czech Summer 1738280/3086045
Czech Summer (jars/mpicbg.jar) 
jars/mpicbg.jar done
Czech Summer (plugins/mpicbg_.jar) 
plugins/mpicbg_.jar done
Czech Summer (jars/Jama.jar) 
jars/Jama.jar done
Czech Summer (jars/javac.jar) 
jars/javac.jar done
Done: Czech Summer

Skipping locally-modified jars/ij.jar
Not updating jars/mpicbg.jar (INSTALLED)

(process:24381): GConf-WARNING **: Client failed to connect to the D-BUS daemon:
Unable to autolaunch a dbus-daemon without a $DISPLAY for X11
GConf Error: No D-BUS daemon running

Downloading... (plugins/mpicbg_.jar) 
plugins/mpicbg_.jar done
Done: Downloading...

Installed plugins/mpicbg_.jar
Skipping locally-modified jars/Jama.jar
Skipping locally-modified jars/javac.jar
Building plugins/FS_Align_TrakEM2.jar <- src-plugins/FS_Align_Trak...
Compiling 5 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/FS_Align_TrakEM2
Building plugins/Calculator_Plus.jar <- src-plugins/Calculator_Plus/
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Calculator_Plus
Building plugins/BeanShell_Interpreter.jar <- src-plugins/BeanShel...
Warning: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/java/linux-amd64/jdk1.6.0_24/jre/../lib/tools.jar overrides com.sun>tools

Warning: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/java/linux-amd64/jdk1.6.0_24/jre/../lib/tools.jar overrides com.sun>tools

Compiling 25 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/fiji-compat
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 3 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/fiji-scripting
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 2 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/BeanShell_Interpreter
Building plugins/Reconstruct_Reader.jar <- src-plugins/Reconstruct...
Compiling 9 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Reconstruct_Reader
Building plugins/Sync_Win.jar <- src-plugins/Sync_Win/
Compiling 12 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Sync_Win
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Sync_Win/src/main/java/Sync_Windows.java uses or overrides 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.
Building plugins/PointPicker_.jar <- src-plugins/PointPicker_/
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/PointPicker_
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/PointPicker_/src/main/java/PointPicker_.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Building plugins/AnalyzeSkeleton_.jar <- src-plugins/AnalyzeSkelet...
Compiling 6 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/AnalyzeSkeleton_
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/AnalyzeSkeleton_/src/main/java/skeleton_analysis/AnalyzeSkeleton_.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Building plugins/Gray_Morphology.jar <- src-plugins/Gray_Morphology/
Compiling 5 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Gray_Morphology
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Gray_Morphology/src/main/java/mmorpho/LocalHistogram.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Building plugins/Descriptor_based_registration.jar <- src-plugins/...
Compiling 26 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/fiji-lib
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/fiji-lib/src/main/java/fiji/util/gui/JFrameCommandFinder.java uses or overrides 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 /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/pal-optimization
Compiling 190 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/VIB-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 121 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/3D_Viewer
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 32 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:16: warning: unmappable character for encoding ASCII
 * J Koenderink and A van Doorn, ???Surface shape and
                                 ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:16: warning: unmappable character for encoding ASCII
 * J Koenderink and A van Doorn, ???Surface shape and
                                  ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:16: warning: unmappable character for encoding ASCII
 * J Koenderink and A van Doorn, ???Surface shape and
                                   ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:17: warning: unmappable character for encoding ASCII
 * curvature scales,??? Image Vision Comput, vol. 10, no. 8,
                    ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:17: warning: unmappable character for encoding ASCII
 * curvature scales,??? Image Vision Comput, vol. 10, no. 8,
                     ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:17: warning: unmappable character for encoding ASCII
 * curvature scales,??? Image Vision Comput, vol. 10, no. 8,
                      ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:18: warning: unmappable character for encoding ASCII
 * pp. 557???565, 1992
          ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:18: warning: unmappable character for encoding ASCII
 * pp. 557???565, 1992
           ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java:18: warning: unmappable character for encoding ASCII
 * pp. 557???565, 1992
            ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java:78: warning: unmappable character for encoding ASCII
	 * Is set to true, then rotate the destination by 90??.
	                                                    ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java:78: warning: unmappable character for encoding ASCII
	 * Is set to true, then rotate the destination by 90??.
	                                                     ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java:724: warning: unmappable character for encoding ASCII
	 * will be rotated 90??.
	                     ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java:724: warning: unmappable character for encoding ASCII
	 * will be rotated 90??.
	                      ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java:732: warning: unmappable character for encoding ASCII
	 * will be be rotated 90??. Cannot be changed after the start() method has been
	                        ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java:732: warning: unmappable character for encoding ASCII
	 * will be be rotated 90??. Cannot be changed after the start() method has been
	                         ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/denoise/ROF_Denoise.java:23: warning: unmappable character for encoding ASCII
 * Based on the Matlab code by Philippe Magiera & Carl L??ndahl:
                                                        ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/Fiji_Plugins/src/main/java/fiji/denoise/ROF_Denoise.java:23: warning: unmappable character for encoding ASCII
 * Based on the Matlab code by Philippe Magiera & Carl L??ndahl:
                                                         ^
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/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.
Note: Recompile with -Xlint:unchecked for details.
17 warnings
Compiling 16 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Opener
Note: /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Opener/src/main/java/spimopener/GaussianStackFocuser.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 137 files in /data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/LocalCoordinateSystemPointDescriptor.java:11: package mpicbg.pointdescriptor.fit does not exist
import mpicbg.pointdescriptor.fit.FitResult;
                                 ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/LocalCoordinateSystemPointDescriptor.java:58: cannot find symbol
symbol  : class FitResult
location: class mpicbg.pointdescriptor.LocalCoordinateSystemPointDescriptor<P>
	public FitResult fitMatches( final ArrayList<PointMatch> matches )  { return null; }
	       ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/SimplePointDescriptor.java:8: package mpicbg.pointdescriptor.fit does not exist
import mpicbg.pointdescriptor.fit.FitResult;
                                 ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/SimplePointDescriptor.java:25: cannot find symbol
symbol  : class FitResult
location: class mpicbg.pointdescriptor.SimplePointDescriptor<P>
	public FitResult fitMatches( final ArrayList<PointMatch> matches ) { return null; }
	       ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantModel.java:6: package mpicbg.pointdescriptor.fit does not exist
import mpicbg.pointdescriptor.fit.FitResult;
                                 ^
/data/devel/jenkins/jobs/Fiji-minimal/workspace/fiji/src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantModel.java:15: cannot find symbol
symbol: class FitResult
public abstract class TranslationInvariantModel< M extends TranslationInvariantModel< M > > extends AbstractModel< M > implements FitResult
                                                                                                                                  ^
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.
6 errors
fiji.build.minimaven.JavaCompiler$CompileError: Compile error: 1
	at fiji.build.minimaven.JavaCompiler.call(JavaCompiler.java:37)
	at fiji.build.minimaven.POM.build(POM.java:221)
	at fiji.build.minimaven.POM.build(POM.java:175)
	at fiji.build.minimaven.POM.buildJar(POM.java:162)
	at fiji.build.SubFake.action(SubFake.java:184)
	at fiji.build.Rule.make(Rule.java:195)
	at fiji.build.Rule.make(Rule.java:175)
	at fiji.build.Rule.makePrerequisites(Rule.java:333)
	at fiji.build.Rule.make(Rule.java:189)
	at fiji.build.Rule.make(Rule.java:175)
	at fiji.build.Fake.make(Fake.java:256)
	at fiji.build.Fake.main(Fake.java:56)
Compile error: 1
	in rule plugins/Descriptor_based_registration.jar <- src-plugins/...
	in rule all <- ImageJ fiji jars/VectorString.jar jars/ij-app.jar ...
Build step 'Execute shell' marked build as failure

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