[ImageJ-builds] Build failed in Jenkins: Fiji-daily #405
jenkins at imagej.net
jenkins at imagej.net
Thu Jul 5 00:09:47 CDT 2012
See <http://jenkins.imagej.net/job/Fiji-daily/405/changes>
Changes:
[Johannes Schindelin] Get rid of the precompiled ImgLib1 .jar files
[Johannes Schindelin] Fix compile error after a recent ImgLib (1!!!) update
[Johannes Schindelin] Bye-bye imglib2-ui
[Johannes Schindelin] MiniMaven: refactor access to the local Maven repository
[Johannes Schindelin] Fiji Build (MiniMaven): make sure to exclude clojure from building
[Johannes Schindelin] Plug a resource leak in MiniMaven
[Johannes Schindelin] Fiji Build: reuse MiniMaven instances
[Johannes Schindelin] MiniMaven: fix thinko
[Stephan Preibisch] Outcommented the stuff that causes problems in between imglib.jar and the imglib submodule
[Albert Cardona] Update the submodule "modules/TrakEM2"
------------------------------------------
[...truncated 5780 lines...]
Note: Recompile with -Xlint:deprecation for details.
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/MTrack2_/src/main/java/MTrack2_.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Building plugins/Jython_Interpreter.jar <- src-plugins/Jython_Inte...
Building plugins/registration_3d.jar <- src-plugins/registration_3d/
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/registration_3d
Building plugins/LocalThickness_.jar <- src-plugins/LocalThickness_/
Compiling 5 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/LocalThickness_
Building plugins/Algorithm_Launcher.jar <- src-plugins/Algorithm_L...
Compiling 3 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Algorithm_Launcher
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Algorithm_Launcher/src/main/java/AlgorithmInfo.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Building plugins/Anisotropic_Diffusion_2D.jar <- src-plugins/Aniso...
Building plugins/Multi_Kymograph.jar <- src-plugins/Multi_Kymograph/
Compiling 4 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Multi_Kymograph
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Building jars/imglib2-algorithms.jar <- jars/imglib2.jar modules/i...
Building in modules/imglib/
Building imglib2-algorithms.jar <- imglib2/algorithms/core/src/mai...
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: ./modules/imglib/imglib2/algorithms/core/src/main/java/net/imglib2/algorithm/gauss/Gauss.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Leaving modules/imglib/
Building jars/imglib2-algorithms-gpl.jar <- jars/imglib2.jar jars/...
Building in modules/imglib/
Building imglib2-algorithms-gpl.jar <- imglib2/algorithms/gpl/src/...
Note: ./modules/imglib/imglib2/algorithms/gpl/src/main/java/net/imglib2/algorithm/region/localneighborhood/DomainCursor.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Leaving modules/imglib/
Building jars/imglib2-io.jar <- plugins/loci_tools.jar jars/imglib...
Building in modules/imglib/
Building imglib2-io.jar <- imglib2/io/src/main/java/net/imglib2/io...
Leaving modules/imglib/
Building plugins/CorrectBleach_.jar <- src-plugins/CorrectBleach_/
Compiling 8 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection_ExpoFit.java:8: warning: unmappable character for encoding ASCII
* Copyright ?? 2010 Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection_ExpoFit.java:8: warning: unmappable character for encoding ASCII
* Copyright ?? 2010 Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection_SimpleRatio.java:13: warning: unmappable character for encoding ASCII
* Copyright ?? 2004, 2005, 2010 Jens Rietdorf, Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection_SimpleRatio.java:13: warning: unmappable character for encoding ASCII
* Copyright ?? 2004, 2005, 2010 Jens Rietdorf, Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection_MH.java:15: warning: unmappable character for encoding ASCII
* Copyright ?? 2010 Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection_MH.java:15: warning: unmappable character for encoding ASCII
* Copyright ?? 2010 Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection.java:22: warning: unmappable character for encoding ASCII
* Copyright ?? 2010 Kota Miura
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/CorrectBleach_/src/main/java/emblcmci/BleachCorrection.java:22: warning: unmappable character for encoding ASCII
* Copyright ?? 2010 Kota Miura
^
8 warnings
Building plugins/Statistical_Region_Merging.jar <- src-plugins/Sta...
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Statistical_Region_Merging
Building plugins/Color_Inspector_3D.jar <- src-plugins/Color_Inspe...
Compiling 4 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Color_Inspector_3D
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Color_Inspector_3D/src/main/java/Color_Inspector_3D.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Building plugins/Javascript_.jar <- src-plugins/Javascript_/
Building jars/imglib-scripting.jar <- jars/ij.jar jars/imglib.jar ...
Building in modules/imglib/
Building imglib-scripting.jar <- imglib1/scripting/src/main/java/s...
Leaving modules/imglib/
Building plugins/SPIM_Opener.jar <- src-plugins/SPIM_Opener/
Building plugins/Fiji_Developer.jar <- src-plugins/Fiji_Developer/
Compiling 5 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Fiji_Developer
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Fiji_Developer/src/main/java/fiji/Wiki_Editor.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Fiji_Developer/src/main/java/fiji/Wiki_Editor.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Building plugins/Colocalisation_Analysis.jar <- src-plugins/Coloca...
Compiling 42 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:171: warning: unmappable character for encoding ASCII
gd2.addNumericField("Pixel Size (??m)", pixelSize,3);
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:171: warning: unmappable character for encoding ASCII
gd2.addNumericField("Pixel Size (??m)", pixelSize,3);
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:660: warning: unmappable character for encoding ASCII
+"\tR(rand) mean??sd"
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:660: warning: unmappable character for encoding ASCII
+"\tR(rand) mean??sd"
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:668: warning: unmappable character for encoding ASCII
if (Costes||rBlocks) strPSF = df3.format(psf*pixelSize*2)+ " ??m ("+df0.format(psf*2)+" pix.)" ;
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:668: warning: unmappable character for encoding ASCII
if (Costes||rBlocks) strPSF = df3.format(psf*pixelSize*2)+ " ??m ("+df0.format(psf*2)+" pix.)" ;
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:672: warning: unmappable character for encoding ASCII
"\t" +df3.format(r2mean) + "??"+ df3.format(r2sd)+
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Test.java:672: warning: unmappable character for encoding ASCII
"\t" +df3.format(r2mean) + "??"+ df3.format(r2sd)+
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Threshold.java:695: warning: unmappable character for encoding ASCII
//[i.e. E(ch1if ch2>0) ?? E(ch1total)]
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Threshold.java:695: warning: unmappable character for encoding ASCII
//[i.e. E(ch1if ch2>0) ?? E(ch1total)]
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Threshold.java:702: warning: unmappable character for encoding ASCII
//[i.e. E(ch1 if ch2>ch2threshold) ?? (Ech1total)]
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Threshold.java:702: warning: unmappable character for encoding ASCII
//[i.e. E(ch1 if ch2>ch2threshold) ?? (Ech1total)]
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Threshold.java:707: warning: unmappable character for encoding ASCII
//[i.e. E(ch1>ch1threshold) ?? E(ch1total)]
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/Colocalisation_Threshold.java:707: warning: unmappable character for encoding ASCII
//[i.e. E(ch1>ch1threshold) ?? E(ch1total)]
^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Colocalisation_Analysis/src/main/java/results/SingleWindowDisplay.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
14 warnings
Building plugins/Interactive_3D_Surface_Plot.jar <- src-plugins/In...
Compiling 12 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:297: warning: unmappable character for encoding ASCII
// IJ.run("Set Scale...", "distance=1.001 known=100 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:297: warning: unmappable character for encoding ASCII
// IJ.run("Set Scale...", "distance=1.001 known=100 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:298: warning: unmappable character for encoding ASCII
// //IJ.run("Set Scale...", "distance=2.2 known=5 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:298: warning: unmappable character for encoding ASCII
// //IJ.run("Set Scale...", "distance=2.2 known=5 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:299: warning: unmappable character for encoding ASCII
IJ.run("Set Scale...", "distance=12 known=100 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:299: warning: unmappable character for encoding ASCII
IJ.run("Set Scale...", "distance=12 known=100 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:300: warning: unmappable character for encoding ASCII
// //IJ.run("Set Scale...", "distance=30 known=0.5 pixel=1 unit=??m");
^
/data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Interactive_3D_Surface_Plot/src/main/java/Interactive_3D_Surface_Plot.java:300: warning: unmappable character for encoding ASCII
// //IJ.run("Set Scale...", "distance=30 known=0.5 pixel=1 unit=??m");
^
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.
8 warnings
Building plugins/Analyze_Reader_Writer.jar <- src-plugins/Analyze_...
Compiling 2 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Analyze_Reader_Writer
Building plugins/Time_Stamper.jar <- src-plugins/Time_Stamper/
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Time_Stamper
Building plugins/RATS_.jar <- src-plugins/RATS_/
Compiling 3 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/RATS_
Building plugins/Kuwahara_Filter.jar <- src-plugins/Kuwahara_Filter/
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Kuwahara_Filter
Building plugins/SplineDeformationGenerator_.jar <- src-plugins/Sp...
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/SplineDeformationGenerator_
java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at fiji.build.Fake.callJavac(Fake.java:551)
at fiji.build.MiniMaven$POM.build(MiniMaven.java:490)
at fiji.build.MiniMaven$POM.buildJar(MiniMaven.java:421)
at fiji.build.SubFake.action(SubFake.java:169)
at fiji.build.Rule.make(Rule.java:195)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Rule.makePrerequisites(Rule.java:331)
at fiji.build.Rule.make(Rule.java:189)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Fake.make(Fake.java:265)
at fiji.build.Fake.main(Fake.java:55)
Caused by: java.lang.OutOfMemoryError: Java heap space
Could not find javac java.lang.reflect.InvocationTargetException (tools path = null), falling back to system javac
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/SplineDeformationGenerator_/src/main/java/SplineDeformationGenerator/SplineDeformationGenerator_.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/SplineDeformationGenerator_/src/main/java/SplineDeformationGenerator/SplineDeformationGenerator_.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Building jars/imglib-io.jar <- plugins/loci_tools.jar jars/imglib....
Building in modules/imglib/
Building imglib-io.jar <- imglib1/io/src/main/java/mpicbg/imglib/i...
java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at fiji.build.Fake.callJavac(Fake.java:551)
at fiji.build.Fake.compileJavas(Fake.java:637)
at fiji.build.Rule.compileJavas(Rule.java:409)
at fiji.build.CompileJar.action(CompileJar.java:56)
at fiji.build.Rule.make(Rule.java:195)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Fake.fakeOrMake(Fake.java:1129)
at fiji.build.SubFake.fakeOrMake(SubFake.java:203)
at fiji.build.SubFake.action(SubFake.java:164)
at fiji.build.Rule.make(Rule.java:195)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Rule.makePrerequisites(Rule.java:331)
at fiji.build.Rule.make(Rule.java:189)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Fake.make(Fake.java:265)
at fiji.build.Fake.main(Fake.java:55)
Caused by: java.lang.OutOfMemoryError: Java heap space
Could not find javac java.lang.reflect.InvocationTargetException (tools path = null), falling back to system javac
Leaving modules/imglib/
Building plugins/JRuby_Interpreter.jar <- src-plugins/JRuby_Interp...
Building plugins/Action_Bar.jar <- src-plugins/Action_Bar/
Compiling 1 files in /data/devel/jenkins/jobs/Fiji-daily/workspace/src-plugins/Action_Bar
Compile error
at fiji.build.Fake.callJavac(Fake.java:554)
at fiji.build.MiniMaven$POM.build(MiniMaven.java:490)
at fiji.build.MiniMaven$POM.buildJar(MiniMaven.java:421)
at fiji.build.SubFake.action(SubFake.java:169)
at fiji.build.Rule.make(Rule.java:195)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Rule.makePrerequisites(Rule.java:331)
at fiji.build.Rule.make(Rule.java:189)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Fake.make(Fake.java:265)
at fiji.build.Fake.main(Fake.java:55)
Compile error
at fiji.build.Fake.callJavac(Fake.java:554)
at fiji.build.MiniMaven$POM.build(MiniMaven.java:490)
at fiji.build.MiniMaven$POM.buildJar(MiniMaven.java:421)
at fiji.build.SubFake.action(SubFake.java:169)
at fiji.build.Rule.make(Rule.java:195)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Rule.makePrerequisites(Rule.java:331)
at fiji.build.Rule.make(Rule.java:189)
at fiji.build.Rule.make(Rule.java:175)
at fiji.build.Fake.make(Fake.java:265)
at fiji.build.Fake.main(Fake.java:55)
Compile error
in rule plugins/Action_Bar.jar <- src-plugins/Action_Bar/
in rule all <- ImageJ fiji jars/ij.jar plugins/loci_tools.jar jar...
Build step 'Execute shell' marked build as failure
Archiving artifacts
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