[ImageJ-builds] Build failed in Jenkins: Fiji-daily #456
jenkins at imagej.net
jenkins at imagej.net
Sun Aug 19 00:02:45 CDT 2012
See <http://jenkins.imagej.net/job/Fiji-daily/456/>
------------------------------------------
[...truncated 1093 lines...]
[copy] Copying 10 files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/scifio/build/src
[copy] Copying 206 files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/scifio/build/src
[copy] Copying 12 files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/scifio/build/classes
[copy] Copied 14 empty directories to 10 empty directories under /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/scifio/build/classes
compile:
[javac] Compiling 196 source files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/scifio/build/classes
[javac] /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/scifio/build/src/loci/formats/itk/ITKBridgeJNI.java:141: warning: [deprecation] asRetrieve(loci.formats.meta.MetadataStore) in loci.formats.MetadataTools has been deprecated
[javac] MetadataRetrieve retrieve = MetadataTools.asRetrieve(reader.getMetadataStore());
[javac] ^
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 1 warning
scifio.jar:
[jar] Building jar: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/scifio.jar
deps-formats:
jar-formats:
init-title:
[echo] ----------=========== bio-formats ===========----------
init-timestamp:
init-version:
init-manifest-cp:
init:
copy-source:
[copy] Copying 1 file to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/src
[copy] Copying 133 files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/src
[copy] Copying 1 file to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/classes
[copy] Copied 6 empty directories to 3 empty directories under /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/classes
compile:
[javac] Compiling 131 source files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/classes
[javac] /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/src/loci/formats/in/TrestleReader.java:322: warning: [deprecation] isOMEXMLMetadata(java.lang.Object) in loci.formats.MetadataTools has been deprecated
[javac] if (MetadataTools.isOMEXMLMetadata(store) ||
[javac] ^
[javac] /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/bio-formats/build/src/loci/formats/in/TrestleReader.java:323: warning: [deprecation] isOMEXMLRoot(java.lang.Object) in loci.formats.MetadataTools has been deprecated
[javac] MetadataTools.isOMEXMLRoot(store.getRoot()))
[javac] ^
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 2 warnings
formats.jar:
[jar] Building jar: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/bio-formats.jar
deps-loci-plugins:
jar-loci-plugins:
init-title:
[echo] ----------=========== loci_plugins ===========----------
init-timestamp:
init-version:
init-manifest-cp:
init:
copy-source:
[copy] Copying 82 files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/loci-plugins/build/src
[copy] Copying 3 files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/loci-plugins/build/classes
[copy] Copied 10 empty directories to 5 empty directories under /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/loci-plugins/build/classes
compile:
[javac] Compiling 71 source files to /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/components/loci-plugins/build/classes
loci-plugins.jar:
[jar] Building jar: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/loci_plugins.jar
tools:
[echo] ----------=========== loci_tools ===========----------
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/bio-formats.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/clibwrapper_jiio.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/forms-1.3.0.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/jai_imageio.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/loci-common.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/loci_plugins.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/mdbtools-java.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/metakit.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/netcdf-4.0.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/ome-xml.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/poi-loci.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/serializer-2.7.1.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/scifio.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/xalan-2.7.1.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/slf4j-api-1.5.10.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/slf4j-log4j12-1.5.10.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[unjar] Expanding: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/log4j-1.2.15.jar into /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
[jar] Building jar: /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/artifacts/loci_tools.jar
[delete] Deleting directory /data/devel/jenkins/jobs/Fiji-daily/workspace/modules/bio-formats/loci-tools
BUILD SUCCESSFUL
Total time: 22 seconds
Building loci_tools.jar <- artifacts/loci_tools.jar
Leaving modules/bio-formats/
Building plugins/TrakEM2_.jar <- jars/ij.jar jars/jai_core.jar jar...
Building in modules/TrakEM2/
Building TrakEM2_.jar <- ini/trakem2/imaging/filters/LUTRed.java m...
./modules/TrakEM2/ini/trakem2/display/Patch.java:102: package mpicbg.imglib.image.display.imagej does not exist
import mpicbg.imglib.image.display.imagej.ImageJFunctions;
^
./modules/TrakEM2/ini/trakem2/imaging/StitchingTEM.java:44: package mpicbg.imglib.algorithm.fft does not exist
import mpicbg.imglib.algorithm.fft.PhaseCorrelationPeak;
^
./modules/TrakEM2/ini/trakem2/utils/AreaUtils.java:38: package mpicbg.imglib.image.display.imagej does not exist
import mpicbg.imglib.image.display.imagej.ImageJFunctions;
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:14: package mpicbg.imglib.algorithm.integral does not exist
import mpicbg.imglib.algorithm.integral.IntegralImage;
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:15: package mpicbg.imglib.algorithm.integral does not exist
import mpicbg.imglib.algorithm.integral.ScaleAreaAveraging2d;
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:250: cannot find symbol
symbol : class ScaleAreaAveraging2d
location: class ini.trakem2.persistence.IntegralImageMipMaps
static private final ScaleAreaAveraging2d<LongType, UnsignedByteType> saa(final byte[] b, final int[] dims) {
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:4: package mpicbg.imglib.algorithm.fft does not exist
import mpicbg.imglib.algorithm.fft.PhaseCorrelation;
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:5: package mpicbg.imglib.algorithm.fft does not exist
import mpicbg.imglib.algorithm.fft.PhaseCorrelationPeak;
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:6: cannot find symbol
symbol : class ImagePlusAdapter
location: package mpicbg.imglib.image
import mpicbg.imglib.image.ImagePlusAdapter;
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:12: cannot find symbol
symbol : class PhaseCorrelationPeak
location: class ini.trakem2.imaging.PhaseCorrelationCalculator
final PhaseCorrelationPeak peak;
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:30: cannot find symbol
symbol : class PhaseCorrelationPeak
location: class ini.trakem2.imaging.PhaseCorrelationCalculator
public PhaseCorrelationPeak getPeak()
^
./modules/TrakEM2/ini/trakem2/display/Patch.java:1851: cannot find symbol
symbol : variable ImageJFunctions
location: class ini.trakem2.display.Patch
ByteProcessor rmask = (ByteProcessor) ImageJFunctions.copyToImagePlus(shapeListImage, ImagePlus.GRAY8).getProcessor();
^
./modules/TrakEM2/ini/trakem2/imaging/StitchingTEM.java:548: cannot find symbol
symbol : class PhaseCorrelationPeak
location: class ini.trakem2.imaging.StitchingTEM
PhaseCorrelationPeak peak = t.getPeak();
^
./modules/TrakEM2/ini/trakem2/utils/AreaUtils.java:499: cannot find symbol
symbol: variable ImageJFunctions
ImagePlus imp = ImageJFunctions.copyToImagePlus(imb, ImagePlus.GRAY8);
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:143: cannot find symbol
symbol : class ScaleAreaAveraging2d
location: class ini.trakem2.persistence.IntegralImageMipMaps
final ScaleAreaAveraging2d<LongType, UnsignedByteType> saai, saam;
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:146: cannot find symbol
symbol : class IntegralImage
location: class ini.trakem2.persistence.IntegralImageMipMaps
final IntegralImage<UnsignedByteType, LongType> oa =
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:147: cannot find symbol
symbol : class IntegralImage
location: class ini.trakem2.persistence.IntegralImageMipMaps
new IntegralImage<UnsignedByteType, LongType>(
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:151: cannot find symbol
symbol : class ScaleAreaAveraging2d
location: class ini.trakem2.persistence.IntegralImageMipMaps
saai = new ScaleAreaAveraging2d<LongType, UnsignedByteType>(
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:156: cannot find symbol
symbol : class IntegralImage
location: class ini.trakem2.persistence.IntegralImageMipMaps
final IntegralImage<UnsignedByteType, LongType> ma = new IntegralImage<UnsignedByteType, LongType>(
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:156: cannot find symbol
symbol : class IntegralImage
location: class ini.trakem2.persistence.IntegralImageMipMaps
final IntegralImage<UnsignedByteType, LongType> ma = new IntegralImage<UnsignedByteType, LongType>(
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:160: cannot find symbol
symbol : class ScaleAreaAveraging2d
location: class ini.trakem2.persistence.IntegralImageMipMaps
saam = new ScaleAreaAveraging2d<LongType, UnsignedByteType>(ma.getResult(), new UnsignedByteType(), dims);
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:251: cannot find symbol
symbol : class IntegralImage
location: class ini.trakem2.persistence.IntegralImageMipMaps
final IntegralImage<UnsignedByteType, LongType> ii =
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:252: cannot find symbol
symbol : class IntegralImage
location: class ini.trakem2.persistence.IntegralImageMipMaps
new IntegralImage<UnsignedByteType, LongType>(
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:256: cannot find symbol
symbol : class ScaleAreaAveraging2d
location: class ini.trakem2.persistence.IntegralImageMipMaps
return new ScaleAreaAveraging2d<LongType, UnsignedByteType>(
^
./modules/TrakEM2/ini/trakem2/persistence/IntegralImageMipMaps.java:268: cannot find symbol
symbol : class ScaleAreaAveraging2d
location: class ini.trakem2.persistence.IntegralImageMipMaps
final ScaleAreaAveraging2d<LongType, UnsignedByteType> saar, saag, saab, saam;
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:16: cannot find symbol
symbol : variable ImagePlusAdapter
location: class ini.trakem2.imaging.PhaseCorrelationCalculator
Image<T> img1 = ImagePlusAdapter.wrap( imp1 );
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:17: cannot find symbol
symbol : variable ImagePlusAdapter
location: class ini.trakem2.imaging.PhaseCorrelationCalculator
Image<S> img2 = ImagePlusAdapter.wrap( imp2 );
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:19: cannot find symbol
symbol : class PhaseCorrelation
location: class ini.trakem2.imaging.PhaseCorrelationCalculator
PhaseCorrelation<T, S> phase = new PhaseCorrelation<T, S>( img1, img2 );
^
./modules/TrakEM2/ini/trakem2/imaging/PhaseCorrelationCalculator.java:19: cannot find symbol
symbol : class PhaseCorrelation
location: class ini.trakem2.imaging.PhaseCorrelationCalculator
PhaseCorrelation<T, S> phase = new PhaseCorrelation<T, S>( img1, img2 );
^
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.
29 errors
Fake failed: Compile error: 1
in rule TrakEM2_.jar <- ini/trakem2/imaging/filters/LUTRed.java m...
in rule plugins/TrakEM2_.jar <- jars/ij.jar jars/jai_core.jar jar...
in rule all <- ImageJ fiji jars/VectorString.jar jars/ij-app.jar ...
Build step 'Execute shell' marked build as failure
Archiving artifacts
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