[ImageJ-builds] Build failed in Jenkins: BigDataViewer #3
jenkins at imagej.net
jenkins at imagej.net
Tue Jul 29 10:39:20 CDT 2014
See <http://jenkins.imagej.net/job/BigDataViewer/3/changes>
Changes:
[Tobias Pietzsch] changed dialog title from "SpimViewer Import" to "Export for BigDataViewer"
[Tobias Pietzsch] getters in SequenceDescription for timepoints, viewsetups, imgloader
[Tobias Pietzsch] rename View to ViewDescription
[Tobias Pietzsch] add TODO
[Tobias Pietzsch] add spim_data dependency
[Tobias Pietzsch] adapt old SequenceDescription abd ViewSetup to look more like the new spim_data
[Tobias Pietzsch] adapt ImgLoader, ViewerImgLoader, AbstractViewerImgLoader to use ViewId and setupId
[Tobias Pietzsch] Hdf5ImageLoader should work with IDs instead of indices now.
[Tobias Pietzsch] refactor and add javadoc to VolatileGlobalCellCache and remove unused member
[Tobias Pietzsch] There are still some compiler errors but the core should be ready for migration to spim_data
[Tobias Pietzsch] remove old bdv spim.data classes
[Tobias Pietzsch] migrate Hdf5ImageLoader and add XmlIoHdf5ImageLoader
[Tobias Pietzsch] minimal SpimData instantiation
[Tobias Pietzsch] migrate SpimSources to spim_data
[Tobias Pietzsch] fix javadoc
[Tobias Pietzsch] basic example shown in viewer
[Tobias Pietzsch] Fix WriteSequenceToHdf5 and Partition handling.
[Tobias Pietzsch] adapt to change in XmlHelpers
[Tobias Pietzsch] CropDialog and CropImgLoader migrated to spim_data
[Tobias Pietzsch] bugfix: WriteSequenceToHdf5 was using ImgLoader instead of BasicImgLoader
[Tobias Pietzsch] simplification in CropDialog
[Tobias Pietzsch] migrate ExportImagePlusPlugin to spim_data
[Tobias Pietzsch] ExportSpimSequencePlugin works with StackImageLoader
[Tobias Pietzsch] export huisken xml hopefully works. not tested yet.
[Tobias Pietzsch] convenience constructors for SequenceDescriptionMinimal and SpimDataMinimal to create copy with different ImgLoader
[Tobias Pietzsch] adapt export of fused data and cell voyager, as well as scripting. all untested.
[Tobias Pietzsch] adapt CATMAID and OpenConnectome ImageLoaders
[Tobias Pietzsch] adapted RemoteImageLoader to spim_data. No more compile errors!
[Tobias Pietzsch] bugfix: when writing partitions mipmap description, only iterate over setups in partition
[Tobias Pietzsch] enable hdf5 deflate compression
[Tobias Pietzsch] bugfix: don't make the export ImgLoaders open() their files
[Tobias Pietzsch] reading and writing of Partitions XmlIoHdf5ImageLoader
[Tobias Pietzsch] add reader for legacy BDV XML files
[Tobias Pietzsch] clean up
[Tobias Pietzsch] use SequenceDescription.setImgLoader() where appropriate
[Tobias Pietzsch] moved MipmapInfo to separate file. Gson serializer for AffineTransform3D. Remote works.
[Tobias Pietzsch] use SpimData exceptions
[Tobias Pietzsch] clean up, add javadoc, address spim_data TODOs
[Tobias Pietzsch] disable "Crop and Save" button while cropping.
[Tobias Pietzsch] remove unnecessary cast, fix typo and formatting
[Tobias Pietzsch] Open <SpimData> datasets that don't have a ViewerImgLoader through wrapper
[Tobias Pietzsch] bugfix: computation of completion ratio for SubTaskProgressWriter
[Tobias Pietzsch] Check that ImgLoader datatype is UnsignedShortType for export to hdf5
[Tobias Pietzsch] bugfix in XmlIoLegacy: timepoints have to be renamed 0,1,...
[Tobias Pietzsch] little tool to print MipmapInfos for a dataset
[Tobias Pietzsch] simplify exception handling by throwing only SpimDataException
[Tobias Pietzsch] temporarily add SPIM_Registration dependency such that the spimreconstruction ImgLoaders are picked up by the annotation indexer
[Tobias Pietzsch] plugin to resave SpimData sequence to HDF5
[Tobias Pietzsch] ViewerPanel doesn't need the cache as a member variable
[Tobias Pietzsch] remove SPIM_registration dependency
[Tobias Pietzsch] implement spimdata ImgLoader interface (such that HDF5 can be used in spimreconstruction)
[Tobias Pietzsch] propose some reasonable mipmap settings for export
[Tobias Pietzsch] PrintSequenceMipmapInfo tool: print normalized voxel scale.
[Tobias Pietzsch] remove unused variabes
[Tobias Pietzsch] propose mipmaps for exporting from ImagePlus, SpimSequence, and FusedData
[Tobias Pietzsch] Having two identical but disctinct subclasses of RealARBGColorConverter avoids
[Stephan Preibisch] made Resave class more generic so that it can be called from other
[Stephan Preibisch] Have to use the super statement to allow any less specialized version of
[Stephan Preibisch] Removed resave plugin. It lives now in
[Tobias Pietzsch] make BigDataViewer a bit more extension friendly
[Tobias Pietzsch] use ReferenceQueue to remove obsolete keys from cache, instead of finalize()
[Tobias Pietzsch] add local maven repository for jhdf5 and update pom to use jhdf5.13.06.2
[Tobias Pietzsch] pull access to hdf5Reader to class HDF5Access
[Tobias Pietzsch] use HDF5Access via interface IHDF5Access
[Tobias Pietzsch] return DimsAndAxistence from IHDF5Access instead of HDF5DataSetInformation
[Tobias Pietzsch] HDF5AccessHack implements IHDF5Access using low-level HDF5 functions and implementation details obtained from jhdf5 by reflection
[Stephan Preibisch] fixed the exporter to work with missing views
[Tobias Pietzsch] LRU cache for open HDF5 datasets to speed up chunk loading.
[Tobias Pietzsch] remove SPIM_Opener dependency
[Tobias Pietzsch] remove local repo and use the jhdf5 deployed in imagej.thirdparty
[Tobias Pietzsch] replace deprecated jhdf5 methods in WriteSequecneToHdf5
[Tobias Pietzsch] introduce "open as virtual stack" checkbox in ImportPlugin
[Tobias Pietzsch] ExportImagePlusPlugIn: make recordable
[Tobias Pietzsch] do not override imglib2 versions in pom
[Tobias Pietzsch] use low-level HDF5 functions to write sequence of MDArrayBlocks without closing the dataset in between
[Tobias Pietzsch] use managed jdom version
[Tobias Pietzsch] handle MissingViews in AbstractSpimSource
[Tobias Pietzsch] parallelize hdf5 export:
[Tobias Pietzsch] put public WriteSequenceToHdf5 methods to the top of the file and add missing javadoc
[Tobias Pietzsch] bugfix: handle seq.getMissingViews() == null in AbstractSpimSource
[Tobias Pietzsch] be less restrictive when construction setup and converter lists
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Downloaded: http://maven.imagej.net/content/repositories/thirdparty/cisd/jhdf5/13.06.2/jhdf5-13.06.2.jar (9051 KB at 9536.5 KB/sec)
[INFO]
[INFO] --- scijava-maven-plugin:0.1.1:set-rootdir (set-rootdir) @ bigdataviewer-core ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.2:create (default) @ bigdataviewer-core ---
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bigdataviewer-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ bigdataviewer-core ---
[INFO] Compiling 131 source files to /data/devel/jenkins/jobs/BigDataViewer/workspace/core/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /data/devel/jenkins/jobs/BigDataViewer/workspace/core/src/main/java/bdv/spimdata/legacy/XmlIoSpimDataMinimalLegacy.java:[123,27] reference to FinalDimensions is ambiguous, both method FinalDimensions(long...) in net.imglib2.FinalDimensions and method FinalDimensions(int...) in net.imglib2.FinalDimensions match
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] BigDataViewer Projects ............................ SUCCESS [3.250s]
[INFO] BigDataViewer Core ................................ FAILURE [4.311s]
[INFO] BigDataViewer Fiji ................................ SKIPPED
[INFO] BigDataServer ..................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8.476s
[INFO] Finished at: Tue Jul 29 10:39:20 CDT 2014
[INFO] Final Memory: 32M/371M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.3.2:compile (default-compile) on project bigdataviewer-core: Compilation failure
[ERROR] /data/devel/jenkins/jobs/BigDataViewer/workspace/core/src/main/java/bdv/spimdata/legacy/XmlIoSpimDataMinimalLegacy.java:[123,27] reference to FinalDimensions is ambiguous, both method FinalDimensions(long...) in net.imglib2.FinalDimensions and method FinalDimensions(int...) in net.imglib2.FinalDimensions match
[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 :bigdataviewer-core
Build step 'Execute shell' marked build as failure
Archiving artifacts
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