[ImageJ-builds] Build failed in Jenkins: ImgLib-daily #1345

jenkins at imagej.net jenkins at imagej.net
Sat Oct 18 00:03:59 CDT 2014 

See <http://jenkins.imagej.net/job/ImgLib-daily/1345/changes>

Changes:

[Stephan Preibisch] imglib2-core: a new Type, UnsignedAnybitType, with arbitrary bit depth.

[Stephan Preibisch] imglib2-core: test for UnsignedAnyBitType

[Stephan Preibisch] imglib2-core: UnsignedAnyBitType now has getBigInteger.

[Stephan Preibisch] imglib-core: UnsignedAnyBitType.setBigInteger

[Stephan Preibisch] imglib2-core: faster implementation for UnsignedAnyBitType.setBigInteger

[Stephan Preibisch] imglib2-core: UnsignedAnyBitType .inc() and .dec() with tests.

[Stephan Preibisch] imglib2-core: UnsignedAnyBitType got its own RealType math methods

[Stephan Preibisch] imglib2-algorithms: IntegralHistogram for 1d and 2d images.

[Stephan Preibisch] imglib2-algorithms: moved IntegralHistogram to scripting package,

[Stephan Preibisch] imglib2-scripting: first attempt at a RandomAccess+Cursor that accesses

[Stephan Preibisch] imglib2-scripting: documentation on Histograms and also fixes.

[Stephan Preibisch] imglib2-scripting: HistogramFeatures is an image that gets filled

[Stephan Preibisch] imglib2-scripting: fixed numerous issues with IntegralHistogram.

[Stephan Preibisch] imglib2-scripting: IntegralHistogram contains IntegerType samples.

[Stephan Preibisch] imglib2-scripting: Histograms is able to iterate properly.

[Stephan Preibisch] imglib2-scripting: HistogramFeatures cleaned up a bit, still doesn't give correct results.

[Stephan Preibisch] imglib2-scripting: tests for piece-wise testing of integral histograms

[Stephan Preibisch] imglib2-scripting: fixed hopefully all errors in integral histograms and their features.

[Stephan Preibisch] imglib2-scripting: integral histogram and features without the debugging.

[Stephan Preibisch] imglib2-scripting: make Histograms return a long[]

[Stephan Preibisch] imglib2-scripting: integral histogram now accepts an arbitrary type

[Stephan Preibisch] imglib2-scripting: faster features from integral histogram.

[Stephan Preibisch] imglib2-scripting: added IHStdDev, computed from integral histogram.

[Stephan Preibisch] imglib2-scripting: Histograms now return Histogram at get().

[Stephan Preibisch] imglib2-scripting: refactored integral histograms.

[Stephan Preibisch] imglib2-scripting: IHMedian is now more correctly estimated.

[Stephan Preibisch] imglib2-scripting: more refactoring for integral histograms.

[Stephan Preibisch] imglib2-scripting: compute StdDev in ExampleIntegralHistogram with means instead of medians.

[Stephan Preibisch] imglib2-scripting: Histogram takes nBins as argument

[Stephan Preibisch] imglib2-scripting: refactored integral histogram classes to be type-friendly

[Stephan Preibisch] imglib2-scripting: removing obsolete comments.

[Stephan Preibisch] imglib-scripting: implemented n-d integral histogram

[Stephan Preibisch] imglib2-scripting: integral histogram populate2 (2d) is a bit faster,

[Stephan Preibisch] imglib2-scripting: Histogram.computeBin returns a long instead of an int.

[Stephan Preibisch] imglib2-scripting: populateND for integral histogram works correctly.

[Stephan Preibisch] imglib2-scripting: more tests for integral histograms

[Stephan Preibisch] imglib2-scripting: removed lots of debugging statements and commented out code

[Stephan Preibisch] imglib2-scripting: removed imports

[Stephan Preibisch] imglib2-scripting: faster 2d and nd integral histogram by using fwd(dim) rather than move(1, dim)

[Stephan Preibisch] imglib2-scripting: removed commented out code

[Stephan Preibisch] imglib2-scripting: FastIntegralImg beats to pulp the IntegralImg

[Stephan Preibisch] imglib2-scripting: FastIntegralImg has now specialized method

[Stephan Preibisch] imglib2-scripting: attempt at speeding up the nd case of FastIntegralImg

[Stephan Preibisch] imglib2-scripting: convenience methods and contructors for FastIntegralImg.

[Stephan Preibisch] imglib2-scripting: IntegralCursor and ExampleIntegralImageFeatures,

[Stephan Preibisch] imglib2-core: UnsignedBit64Type, a Type with arbitrary bit depths 1-64.

[Stephan Preibisch] imglib2-score: very small, but real, performance improvements for UnsignedBit64Type.

[Stephan Preibisch] imglib-core test: UnsignedBit64Type for 1 bit and BitType perform the same.

[Stephan Preibisch] imglib2-core: Unsigned2BitType and Unsigned4BitType, with a test.

[Stephan Preibisch] imglib2-core: new type UnsignedLongType,  with a test.

[Stephan Preibisch] imglib2-core: proper header documentation for Unsigned2BitType and Unsigned4BitType

[Stephan Preibisch] Added a BitArray64 that uses long as basis

[Stephan Preibisch] Removed BitArray64 and changed BitArray to 64 bit

[Stephan Preibisch] imglib-core: Unsigned128BitType, with Type math implemented using BigInteger,

[Stephan Preibisch] imglib2-core: edited documentation for Unsigned128BitInteger

[Stephan Preibisch] imglib2-core: removed unused, irrelevant code from UnsignedLongType

[Stephan Preibisch] imglib2-core: UnsignedLongType.div is now implemented properly.

[Stephan Preibisch] imglib2-core: clearer UnsignedLongType.div method, with static divide helper.

[Stephan Preibisch] imglib2-core: proper division for UnsignedBit64Type

[Stephan Preibisch] imglib2-core: UnsignedBit64Type.compareTo is now proper.

[Stephan Preibisch] Changed int entitiesPerPixel to Fractional values

[Stephan Preibisch] imglib2-core: adapted to Fraction the 2-bit, 4-bit, any-bit, bit-64,

[Stephan Preibisch] imglib2-core: Unsigned2BitType and Unsigned4BitType are ~15% faster,

[Stephan Preibisch] imglib2-core: Unsigned2BitType and Unsinged4BitType use a long index,

[Stephan Preibisch] imglib2-core: new AbstractBitType that collects common methods from Unsigned2BitType

[Stephan Preibisch] imglib2-core: A test for Unsigned12BitType that proves it overwrites values,

[Stephan Preibisch] imglib2-core: a new Unsigned12BitType2 that actually works

[Stephan Preibisch] imglib2-core: redefined UnsignedBit64Type as extending AbstractBitType.

[Stephan Preibisch] imglib2-core: Unsigned12BitType2 slightly faster.

[Stephan Preibisch] imglib2-core: slightly faster Unsigned2BitType, Unsigned4BitType and UnsignedBit64Type

[Stephan Preibisch] imglib2-core: more extensive test for Unsigned2BitType and Unsigned4BitType

[Stephan Preibisch] imglib2-core: test showing that internal Unsigned12BitType doesn't work,

[Stephan Preibisch] imglib2-scripting: committing changes to tests and comments

[Stephan Preibisch] imglib2-core: removed unused variable from Unsigned12BitType2

[Stephan Preibisch] imglib2-core: removed Unsigned12BitType2

[Stephan Preibisch] imglib2-core: test Unsigned12BitType for its full range 0-4095.

[Stephan Preibisch] imglib2-core: new Unsigned12BitType, based on LongAccess,

[Stephan Preibisch] imglib2-core: fixed errors in Unsigned128BitType and added a test.

[Stephan Preibisch] imglib2-core: less operations for Unsigned128BitType inc()

[Stephan Preibisch] imglib2-core: edited comments

[Stephan Preibisch] Adjusted to the Fraction branch

[Stephan Preibisch] Minor fixes and comments in Albert's BitTypes collection

[Stephan Preibisch] started working on the bittypes

[Stephan Preibisch] manually merged master into albert-dev-fraction (some failed to get rebased properly)

[Stephan Preibisch] updated cellImg to Fraction interface instead of int for entitiesPerPixel

[Stephan Preibisch] introduced new hierarchy for bitwise types

[Stephan Preibisch] updated the fraction class so that it can return the ratio in double

[Stephan Preibisch] fixed Tobias's classes so that the cell size is now based on the Fraction class

[Stephan Preibisch] fixed bug that did not consider fractions

[squareys] Added SubIntervalIterable interface

[squareys] Added IterableTransformBuilder

[squareys] Implementation of SubIntervallIterable for ArrayImg

[squareys] Added AbstractArrayCursor

[squareys] Made IntervalView implement IterableInterval

[squareys] Added AbstractArrayLocalizingCursor

[squareys] Make ArrayCursor extend AbstractArrayCursor

[squareys] Made ArrayLocalizingCursor extend AbstractArrayLocalizingCursor

[squareys] Added ArraySubIntervalCursor

[squareys] Added ArrayLocalizingSubIntervalCursor

[squareys] Added ArrayIterableSubIntervalCursorTest

[squareys] Added SlicingCursor

[squareys] Added PlanarSubsetCursor

[squareys] Added PlanarSubsetLocalizingCursor

[squareys] Added optimized cursor support for PlanarImg

[squareys] Added PlanarIterableSubIntervalCursorTest

[squareys] Implemented SubIntervalIterable for LabelingView

[squareys] Implemented SubIntervalIterable for ImgView

[squareys] Implemented SubIntervalIterable for NativeImgLabeling

[squareys] Added WrappedImg to TransformBuilder.visit( RandomAccessibleInterval )

[squareys] Minor optimization to AbstractArrayLocalizingCursor

[squareys] Added PlanarPlaneSubsetCursor

[squareys] Added PlanarPlaneSubsetLocalizingCursor

[squareys] PlanarImg Subset Cursor optimized for one Plane

[squareys] Fixes and minor optimizations to PlanarSubsetLocalizingCursor

[squareys] Fixes and minor improvements to PlanarPlaneSubsetLocalizinhCursor

[squareys] Fixes and minor improvements to PlanarPlaneSubsetCursor

[squareys] Added asserts in PlanarImg

[squareys] Added AbstractSubIntervalIterableCursorTest

[squareys] Added PlanarIterableSubIntervalCursorTest

[squareys] Added ArrayIterableSubIntervalCursorTest

[squareys] Added IterableSubIntervalBenchmark

[squareys] Fixes and minor improvements to AbstractSubIntervalIterableCursorTest

[squareys] Fixed PlanarSubsetLocalizingCursor

[Tobias Pietzsch] move copyCorsor() and copy() to concrete classes (with concrete return type)

[Tobias Pietzsch] remove unnecessary localize() and getIntPosition() overrides and format code.

[Tobias Pietzsch] formatting

[Tobias Pietzsch] Update IterableSubIntervalBenchmark:

[Tobias Pietzsch] SubIntervalCursor check: require that requested interval is contained. Add more comments.

[Tobias Pietzsch] fix IterableTransformBuilder logic for iterating slices.

[Tobias Pietzsch] formatting

[Tobias Pietzsch] add javadoc

[Stephan Saalfeld] Pending problems with BitType

[Stephan Preibisch] Fixed bug in BitType

[Stephan Preibisch] Test for BitType that reproduces the error

[Stephan Preibisch] Added useful JUnit Test for BitType

[Tobias Pietzsch] move Extended[Real]RandomAccessibleInterval to net.imglib2.view package

[Tobias Pietzsch] move Binning to net.imglib2.util package

[Tobias Pietzsch] removed package net.imglib2.img.constant

[Tobias Pietzsch] removed package net.imglib2.sampler.special

[Tobias Pietzsch] fix javadoc typo

[Tobias Pietzsch] moved KDTree and [Real]PointSampleList into net.imglib2 package

[Tobias Pietzsch] rename net.imglib2.concatenate.Util to ConcatenateUtils

[Tobias Pietzsch] FIXUP: missed this in the KDTree move

[Tobias Pietzsch] FIXUP: ConcatenateUtils

[Tobias Pietzsch] move RandomAccessibleOnRealRandomAccessible into net.imglib2.view package

[Tobias Pietzsch] remove IterableIntervalSubset

[Tobias Pietzsch] remove Location (deprecated, replaced by Point)

[Tobias Pietzsch] move Bounded into net.imglib2.outofbounds package

[Tobias Pietzsch] made FinalDimensions and FinalRealInterval classes final

[Tobias Pietzsch] removed unused generic parameters from Projector interface

[Tobias Pietzsch] renamed iterpolation.neighborsearch.NearestNeighborInterpolator to

[Tobias Pietzsch] clean up InverseDistanceWeightingInterpolator comments

[Tobias Pietzsch] remove unused Triple class.

[Tobias Pietzsch] moved Pair interface to net.imglib2.util

[Tobias Pietzsch] clean up net.imglib2.exception

[Tobias Pietzsch] remove unused position.transform.RealPositionable{Floor|Round}Positionable.

[Tobias Pietzsch] move ImgTestHelper to src/test

[Tobias Pietzsch] multithreading: deprecate Chunk and SimpleMultiThreading, remove Stopable

[Tobias Pietzsch] remove unnecessary @SuppressWarnings

[Tobias Pietzsch] Views.extendRandom() can use Util.getTypeFromInterval() because its source is always a RandomAccessibleInterval

[Tobias Pietzsch] remove ImgTranslationAdapter.

[Tobias Pietzsch] remove type.numeric.ExponentialMathType interface

[Tobias Pietzsch] clean up BenchmarkHelper: median() and best() helper methods are no longer public.

[Tobias Pietzsch] clean up util.Util: remove getTypeFrom[Real]RandomAccess()

[Tobias Pietzsch] clean up util.Util: remove unused setCoordinateRecursive/getRecusriveCoordinates

[Tobias Pietzsch] clean up util.Util: rename computeMedian() to median(), computeMinimum() to min(), etc.

[Tobias Pietzsch] clean up comments

[Tobias Pietzsch] util.Util: add TODOs: stuff that should move to LinAlgHelpers

[Stephan Preibisch] Added JUnit tests for 2, 4 & 12bit types

[Stephan Preibisch] Added Test for Unsigned128BitType

[Stephan Preibisch] Fixed comments in JUnit tests

[Tobias Pietzsch] added squareDistance(a,b) and distance(a,b) to LinAlgHelpers. Removed unused computeDistance() and computeLength() versions from util.Util.

[Stephan Preibisch] Renamed the variable bit length type

[Stephan Preibisch] Fixed issues in BasePairBitType

[Stephan Preibisch] Fixed issues in BasePairCharType

[Stephan Preibisch] Outsourced Operator Type from NumericType to allow for a more fine

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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ImgLib2 Algorithms (Legacy) 2.0.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ imglib2-algorithms-legacy ---
[INFO] Deleting /data/devel/jenkins/jobs/ImgLib-daily/workspace/algorithms/legacy/target
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.2:create (default) @ imglib2-algorithms-legacy ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ imglib2-algorithms-legacy ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /data/devel/jenkins/jobs/ImgLib-daily/workspace/algorithms/legacy/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ imglib2-algorithms-legacy ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 15 source files to /data/devel/jenkins/jobs/ImgLib-daily/workspace/algorithms/legacy/target/classes
[INFO] -------------------------------------------------------------
[WARNING] COMPILATION WARNING : 
[INFO] -------------------------------------------------------------
[WARNING] Note: Some input files use or override a deprecated API.
[WARNING] Note: Recompile with -Xlint:deprecation for details.
[INFO] 2 warnings 
[INFO] -------------------------------------------------------------
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /data/devel/jenkins/jobs/ImgLib-daily/workspace/algorithms/legacy/src/main/java/net/imglib2/algorithm/legacy/fft/PhaseCorrelation.java:[256,53] cannot find symbol
symbol  : method getRecursiveCoordinates(int)
location: class net.imglib2.util.Util
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ImgLib2 Projects .................................. SUCCESS [2.941s]
[INFO] ImgLib2 Core Library .............................. SUCCESS [35.142s]
[INFO] ImgLib2 Metadata Extensions ....................... SUCCESS [2.959s]
[INFO] ImgLib2 Algorithms ................................ SUCCESS [0.533s]
[INFO] ImgLib2 Algorithms ................................ SUCCESS [2.901s]
[INFO] ImgLib2 Algorithms (GPL) .......................... SUCCESS [3.093s]
[INFO] ImgLib2 Algorithms (Legacy) ....................... FAILURE [0.197s]
[INFO] ImgLib2 Operations ................................ SKIPPED
[INFO] ImgLib2 Real Transform ............................ SKIPPED
[INFO] ImgLib2 UI ........................................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 49.057s
[INFO] Finished at: Sat Oct 18 00:03:04 CDT 2014
[INFO] Final Memory: 30M/419M
[INFO] ------------------------------------------------------------------------
[WARNING] The requested profile "java5" could not be activated because it does not exist.
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project imglib2-algorithms-legacy: Compilation failure
[ERROR] /data/devel/jenkins/jobs/ImgLib-daily/workspace/algorithms/legacy/src/main/java/net/imglib2/algorithm/legacy/fft/PhaseCorrelation.java:[256,53] cannot find symbol
[ERROR] symbol  : method getRecursiveCoordinates(int)
[ERROR] location: class net.imglib2.util.Util
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :imglib2-algorithms-legacy
Build step 'Invoke top-level Maven targets' marked build as failure
Archiving artifacts
Publishing Javadoc

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