[ImageJ-builds] Build failed in Jenkins: fiji-windows-core #453
Jenkins Daemon
jenkins at qa.nest-initiative.org
Wed Jul 24 18:25:14 CDT 2013
See <https://qa.nest-initiative.org/job/fiji-windows-core/453/changes>
Changes:
[Johannes Schindelin] Expose the 'Slide Show' plugin from the Macro Interpreter
[stephan.preibisch] Fixed bug in multi-channel bead registration
[stephan.preibisch] fixed another bug in setting up multiple tracks
[ignacio.arganda] Trainable Weka Segmentation: added exception print trace.
[ignacio.arganda] Trainable Weka Segmentation: added log information when loading a classifier fails.
[Johannes Schindelin] Memory & Threads...: Fix ImageJ.cfg writing
[stephan.preibisch] enabled the fusion that computes different output images to load images sequentially
[stephan.preibisch] fixed a bug for the multi-channel registration
[stephan.preibisch] added the option to set the initial viewID
[stephan.preibisch] Added the option to preAlign the views before global optimization
[ignacio.arganda] bUnwarpJ: update stack methods to use modern calls.
[ignacio.arganda] bUnwarpJ: make javadoc comment more clear.
[ignacio.arganda] bUnwarpJ: improve javadoc comments.
[ignacio.arganda] bUnwarpJ: fix bug when using masks included in the input images.
[stephan.preibisch] made some choices for parameters more easy
[stephan.preibisch] added option to select only a few angles for fusion
[Curtis Rueden] Add mailing lists metadata
[stephan.preibisch] introduced a new way how to identify bad tile connections, should not get rid off tiles anymore
[stephan.preibisch] added the option to ignore z
[ignacio.arganda] Trainable Weka Segmentation: fixed bugs in the GUI code.
[jean-yves.tinevez] TrackMate_: v2.0.4: fix a GUI bug noticed by T. Pietzsch
[Curtis Rueden] Image_Expression_Parser: fix dependency version
[stephan.preibisch] fixed threshold for integral image bead based registration
[stephan.preibisch] can provide a current guess of the deconvolved image,
[stephan.preibisch] formalized loading of previous image including range check
[Curtis Rueden] fiji-lib: add NumberParser class
[Curtis Rueden] TrackMate_: fix some dependency versions
[Curtis Rueden] TrackMate_: use fiji-lib's NumberParser
[Curtis Rueden] .gitignore: Add more jar files
[Curtis Rueden] Update imglib submodule pointer
[ignacio.arganda] Trainable Weka Segmentation: fix rank of threshold application.
[Curtis Rueden] Use imglib2.version property for imglib2 deps
[Curtis Rueden] Fix whitespace
[Curtis Rueden] Update Bio-Formats dependencies to 4.4.8
[Curtis Rueden] Use fiji.version property for inter-plugin deps
[ignacio.arganda] Trainable Weka Segmentation: added method to compute the precision and recall based on the pixel classification after warping (only for splits and mergers).
[Curtis Rueden] Tell Maven that pom-scijava is outside the reactor
[Johannes Schindelin] Upgrade TrakEM2 to the newest pom-scijava version
[stephan.preibisch] updated deconvolution to the "final" state
[Johannes Schindelin] Use shorter URL in download-launchers
[Johannes Schindelin] Follow ImageJ2's SNAPSHOT versions for now
[Johannes Schindelin] Remove the TrakEM2 module for now
[Johannes Schindelin] Update the ImageJ2 submodule
[Johannes Schindelin] Aaargh... update TrakEM2 to a temporary fork
[stephan.preibisch] fixed a bug in the weighting scheme, normalizing only if sumweights > 1,
[mail] 3D Objects Counter: be less impolite
[Johannes Schindelin] Move resource back where it belongs
[stephan.preibisch] it is now possible to load and store PSFs, makes it much more useful
[ignacio.arganda] Trainable Weka Segmentation: corrected method to calculate precision recall.
[Curtis Rueden] Fix up the README a bit
[Curtis Rueden] README.md: also add Kota
[steinbac] Multi_View_Deconvolution: added new logic to select the standard GPU on multi-GPU hosts
[steinbac] LRFFTThreads: changed println labels for timings per iteration to state which steps are conducted on the CPU and which are done on the GPU
[jenkins] Bump to pom-scijava 1.49
[jenkins] Bump to pom-scijava 1.50
[jenkins] Bump to pom-scijava 1.51
[Curtis Rueden] Update ImageJ2 submodule for pom-scijava 1.51
[Johannes Schindelin] Move to release-coupling with ImageJ2, ImgLib2
[Johannes Schindelin] Stop handling uncoupled submodules
[Johannes Schindelin] Build.sh: refactor the use of maven-helper.sh
[Johannes Schindelin] Build.sh: no need to force-install the SSH uploader
[Johannes Schindelin] Build.sh: use the correct MiniMaven version
[Johannes Schindelin] Ignacio wins the prize
[Johannes Schindelin] Add a few more authors to the README
[jean-yves.tinevez] Descriptor-based registration: propagate single model to multiple time-points
[Johannes Schindelin] Build.sh: clarify the parameter order of uptodate()
[Johannes Schindelin] Build.sh: Make sure that maven-helper.sh is updated properly
[Johannes Schindelin] Build.sh: avoid Git's 'Already up-to-date' cluttering version numbers
[Johannes Schindelin] Build.sh: if scijava-common could not be updated, fail
[Johannes Schindelin] Build.sh: really redirect 'Already up-to-date' message
[Johannes Schindelin] Build.sh: avoid unnecessary call to maven_helper
[Johannes Schindelin] Build.sh: make sure that just-downloaded files are considered up-to-date
[Johannes Schindelin] download-launchers: fix the version of the ij-launcher.jar
[Johannes Schindelin] Build.sh: download launcher releases instead of snapshots
[stephan.preibisch] allow the fusion using the first image as bounding box
[stephan.preibisch] fixed bugs int selecting the standard CUDA device
[stephan.preibisch] allow nearestneighborinterpolation for fusion of datasets
[stephan.preibisch] added the option also for time series
[Johannes Schindelin] Make Make_Screencast.bsh truly executable
[Johannes Schindelin] Refactor Make_Screencast.bsh
[Johannes Schindelin] Make_Screencast (cmd-line): allow specifying a region
[Johannes Schindelin] Make_Screencast (cmd-line): allow specifying the frames per second
[Johannes Schindelin] Make_Screencast (cmd-line): allow overwriting existing files
[Johannes Schindelin] Fix install-java3d
[Johannes Schindelin] Special-case MacOSX in Edit>Memory & Threads... again
[ignacio.arganda] Analyze Skeleton: fixed bug when pruning end-point branches on an image without end points reported by Jan Eglinger.
[Johannes Schindelin] Fix second (and later) runs of Temporal-Color Code
[Johannes Schindelin] Build.sh: work around Git for Windows' lack of stat(1)
[Johannes Schindelin] Build.sh: respect the -- option separator
[Johannes Schindelin] Build.sh: propagate the '-x' to other shell scripts
[stephan.preibisch] fixed two bugs in the overlay fusion for the descriptor based registration
[Johannes Schindelin] Updater_Fix.js: Make sure that ij.IJ is found
[Johannes Schindelin] Add a little utility to update the URLs in Updater_Fix.js
[Johannes Schindelin] Update the URLs in Updater_Fix.js to the newest, latest & greatest
[ignacio.arganda] Trainable Weka Segmentation: added method to create instances in place.
[ignacio.arganda] Trainable Weka Segmentation: create instances in place to improve speed.
[stephan.preibisch] difference-of-mean does not ignore minmaxset anymore
[Johannes Schindelin] QuickPALM: fix NullPointerException
[Johannes Schindelin] Build.sh: handle 'fiji' and 'ImageJ' target again
[Johannes Schindelin] Update .gitignore for current ImageJ2
[Johannes Schindelin] Weed out .gitignore some
[Johannes Schindelin] fiji.Main: Make sure that the IJ1Patcher has run
[ignacio.arganda] Trainable Weka Segmentation: beautify code.
[ignacio.arganda] Trainable Weka Segmentation: clean code.
[ignacio.arganda] Trainable Weka Segmentation: speed classification.
[ignacio.arganda] Trainable Weka Segmentation: fix bug to prevent getting probabilities after changing classifier in the settings dialog.
[ignacio.arganda] Trainable Weka Segmentation: disable unusable buttons after changing classifier in the settings dialog.
[jenkins] Bump to pom-scijava 1.53
[Johannes Schindelin] Fix a couple of compiler warnings in fiji-compat's IJ1 hacking code
[Johannes Schindelin] Make sure that ImageJ2's legacy layer gets initialized
[Johannes Schindelin] IJHacker: be nice if ij-legacy already defined some classes
[Johannes Schindelin] Add ij-app as a dependency of fiji-compat
[Johannes Schindelin] Add Help>Switch To Modern Mode
[Johannes Schindelin] Remove some unused imports
[Johannes Schindelin] JavassistHelper: do not rely on isFrozen
[Johannes Schindelin] fiji-compat's Mighty Mouse handling moved to ij-legacy
[Johannes Schindelin] fiji-compat's CompositeImage handling moved to ij-legacy
[Johannes Schindelin] fiji-compat's ImagePlus handling moved to ij-legacy
[Johannes Schindelin] Some of fiji-compat's ij.IJ handling moved to ij-legacy
[Johannes Schindelin] fiji-compat: setting the context class loader moved to ij-legacy
[Johannes Schindelin] IJ1Patcher: legacy headless support moved to ImageJ2
[Johannes Schindelin] IJHacker: code to set the application name moved to ImageJ2
[Johannes Schindelin] Organize imports in FijiClassLoader
[Johannes Schindelin] fiji-compat: move NoSuchMethodError handling to ij-legacy
[Johannes Schindelin] Fix compiler warnings in CheckClassVersions
[Johannes Schindelin] Fix compiler warnings in User_Plugins
[Johannes Schindelin] Fix compiler warnings in FijiClassLoader
[Johannes Schindelin] Fix compiler warnings in fiji.Main
[Johannes Schindelin] Fix compiler warnings in OtherInstance
[Johannes Schindelin] Fix compiler warnings in SetIcon
[Johannes Schindelin] Fix compiler warnings in fiji.command.Command
[Johannes Schindelin] Fix compiler warnings in IJ_Alt_Key_Listener
[Johannes Schindelin] Fix compiler warnings in SimpleExecuter
[Johannes Schindelin] Fix compiler warnings in FileDialogDecorator
[Johannes Schindelin] Deprecate SimpleExecuter
[Johannes Schindelin] Avoid using the SimpleExecuter
[Johannes Schindelin] Stop forcing IJ.getClassLoader() to return a FijiClassLoader
[Johannes Schindelin] Deprecate the FijiClassLoader
[Johannes Schindelin] Retire fiji.command.Command
[Johannes Schindelin] Bu-bye, ImageJA
[Johannes Schindelin] fiji-compat: move GenericDialog patches to ij-legacy
[Johannes Schindelin] fiji-compat: move NonModalGenericDialog patches to ij-legacy
[Johannes Schindelin] JavassistHelper#verify: avoid using the deprecated FijiClassLoader
[Johannes Schindelin] Add the getMenuItem() function family to FijiTools
[Johannes Schindelin] Also move User_Plugins#installPlugin() to FijiTools
[Johannes Schindelin] Moved another ImageJ 1.x patch to ij-legacy
[Johannes Schindelin] Move the ImageJ 1.x windows' icon logic to ij-legacy
[Johannes Schindelin] Remove the OtherInstance logic from fiji-compat
[Johannes Schindelin] fiji-compat: -batch-no-exit handling moved to ij-legacy
[Johannes Schindelin] Move the prefsDir handling to ij-legacy
[Johannes Schindelin] Move Toolbar handling from fiji-compat to ij-legacy
[Johannes Schindelin] fiji-compat: move the JavaScriptEvaluator patching to ij-legacy
[Johannes Schindelin] fiji-compat: move the Bio-Formats detection patch to ij-legacy
[Johannes Schindelin] fiji-compat: move the symlink fix for DragAndDrop to ij-legacy
[Johannes Schindelin] fiji-compat: remove WindowManager#setCurrentWindow(ImageWindow, boolean)
[Johannes Schindelin] Move fiji-compat's ij.macro.Function#call() patch to ij-legacy
[Johannes Schindelin] Move File>Import>Image Sequence patching to ij-legacy
[Johannes Schindelin] Port fiji-compat's ij.macro.Interpreter patch to ij-legacy
[Johannes Schindelin] Stop special-casing Fiji for Open StartupMacros
[Johannes Schindelin] No longer patch ImageJ 1.x to know about StartupMacros.fiji.ijm
[Johannes Schindelin] fiji-compat: move all HTTPS handling to ij-legacy
[Johannes Schindelin] fiji-compat: move Script Editor hooks to ij-legacy
[Johannes Schindelin] Rename gentlyRunPlugIn() into a less German name
[Johannes Schindelin] Move User_Plugins#runPlugIn() to Main
[Johannes Schindelin] fiji.Main: document runPlugInGently()
[Johannes Schindelin] Move the Fiji-specific Refresh Menus handling into its own plugin
[Johannes Schindelin] Make MenuRefresher a Runnable
[Johannes Schindelin] Use the new LegacyExtensions#runAfterRefreshMenus()
[Johannes Schindelin] Retire the IJHacker
[Johannes Schindelin] Fix a comment
[Johannes Schindelin] Automatically create a modern ImageJ context upon startup
[Johannes Schindelin] Fix ./fiji --run 'Switch to Modern Mode'
[Johannes Schindelin] Fix-Updater: Bump the versions to the current ones
[Johannes Schindelin] Fiji Updater: use the remote bootstrap.js
[Johannes Schindelin] Fiji_Updater: deprecate unused classes
[Johannes Schindelin] Fix 'Align by line ROI' without scaling but with rotation
[Johannes Schindelin] Deprecate the JavassistHelper
[clackn] allow to save matched points and models into the descriptor parameters
[jenkins] Bump to pom-scijava 1.54
[jenkins] Bump to pom-scijava 1.55
[stephan.preibisch] fixed a bug in the fusion that creates different output images
[stephan.preibisch] removed unnecessary debug messages and comment
[jenkins] Bump to pom-scijava 1.56
[Johannes Schindelin] .mailmap: attribute two more email addresses properly
[Johannes Schindelin] Fix scope of all those JUnit dependencies
[stephan.preibisch] fixed a bug in the FIBSEM reader, there was a wrong offset
[jenkins] Bump to pom-scijava 1.57
[Johannes Schindelin] Move all unit tests into the appropriate src/test/java/
[Johannes Schindelin] Touch up the first section of the README
[Johannes Schindelin] README: Mention ImageJ.sh
[Johannes Schindelin] VIB-lib (unit tests): do not expect the test data to be there
[Johannes Schindelin] fiji-compat: temporarily fix integration test
[jenkins] Bump to pom-scijava 1.58
[Johannes Schindelin] Colocalization Analysis (unit tests): move two forgotten classes
[Johannes Schindelin] Colocalization Analysis (unit tests): do not expect test data to be present
[Johannes Schindelin] Add missing file for JEP tests
[Johannes Schindelin] Increase tolerance to let IEP test pass
[Johannes Schindelin] Fix unit test errors in Simple Neurite Trace due to missing test data
[Johannes Schindelin] Turn integration test into a maven-failsafe-plugin based one
[Johannes Schindelin] README: fix mark-down mark-up
[Johannes Schindelin] README: replace double-space after full stop with a single one
------------------------------------------
[...truncated 26924 lines...]
+ option=--mini-maven
+ case "$dashdash,$option" in
+ main_class=imagej.build.MiniMaven
+ shift
+ test 4 -gt 0
+ option=-Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core
+ case "$dashdash,$option" in
++ sq_quote -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core
++ echo -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
+ java_options=' -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core'
+ shift
+ test 3 -gt 0
+ option=-Dminimaven.updateinterval=1
+ case "$dashdash,$option" in
++ sq_quote -Dminimaven.updateinterval=1
++ echo -Dminimaven.updateinterval=1
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
+ java_options=' -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1'
+ shift
+ test 2 -gt 0
+ option=-DartifactId=verbose=true
+ case "$dashdash,$option" in
++ sq_quote -DartifactId=verbose=true
++ echo -DartifactId=verbose=true
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
+ java_options=' -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1 -DartifactId=verbose=true'
+ shift
+ test 1 -gt 0
+ option=install
+ case "$dashdash,$option" in
++ sq_quote install
++ echo install
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
+ java_options=' -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1 -DartifactId=verbose=true install'
+ shift
+ test 0 -gt 0
+ case "$dashdash" in
+ ij_options=' -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1 -DartifactId=verbose=true install'
+ java_options=
+ case "$main_class,`get_first $ij_options`" in
++ get_first -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1 -DartifactId=verbose=true install
++ echo -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core
+ test -z ''
+ case "$main_class" in
+ for path in '"$FIJI_ROOT"/jars/*.jar' '"$FIJI_ROOT"/plugins/*.jar'
+ add_classpath c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar
+ for arg in '"$@"'
+ test -z ''
+ CLASSPATH=c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar
+ for path in '"$FIJI_ROOT"/jars/*.jar' '"$FIJI_ROOT"/plugins/*.jar'
+ add_classpath c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar
+ for arg in '"$@"'
+ test -z c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar
+ CLASSPATH='c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar'
+ for path in '"$FIJI_ROOT"/jars/*.jar' '"$FIJI_ROOT"/plugins/*.jar'
+ add_classpath c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar
+ for arg in '"$@"'
+ test -z 'c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar'
+ CLASSPATH='c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar'
+ for path in '"$FIJI_ROOT"/jars/*.jar' '"$FIJI_ROOT"/plugins/*.jar'
+ add_classpath c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar
+ for arg in '"$@"'
+ test -z 'c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar'
+ CLASSPATH='c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar'
+ for path in '"$FIJI_ROOT"/jars/*.jar' '"$FIJI_ROOT"/plugins/*.jar'
+ add_classpath c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar
+ for arg in '"$@"'
+ test -z 'c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar'
+ CLASSPATH='c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar'
+ for path in '"$FIJI_ROOT"/jars/*.jar' '"$FIJI_ROOT"/plugins/*.jar'
+ add_classpath 'c:/jenkins/workspace/fiji-windows-core/plugins/*.jar'
+ for arg in '"$@"'
+ test -z 'c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar'
+ CLASSPATH='c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar;c:/jenkins/workspace/fiji-windows-core/plugins/*.jar'
+ case "$dry_run" in
++ sq_quote c:/jenkins/workspace/fiji-windows-core
++ echo c:/jenkins/workspace/fiji-windows-core
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
+ FIJI_ROOT_SQ=c:/jenkins/workspace/fiji-windows-core
+ EXECUTABLE_NAME=/c/jenkins/workspace/fiji-windows-core/bin/ImageJ.sh
+ case "$EXECUTABLE_NAME" in
++ expr /c/jenkins/workspace/fiji-windows-core/bin/ImageJ.sh : '.*/\([^/]*\)'
+ EXECUTABLE_NAME=ImageJ.sh
+ EXT_OPTION=
+ case "`uname -s`" in
++ uname -s
++ sq_quote 'c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar;c:/jenkins/workspace/fiji-windows-core/plugins/*.jar'
++ echo 'c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar;c:/jenkins/workspace/fiji-windows-core/plugins/*.jar'
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
++ sq_quote ImageJ.sh
++ echo ImageJ.sh
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
++ sq_quote ImageJ.sh
++ echo ImageJ.sh
++ sed 's/[]"\'\''\\(){}[\!$ ;]/\\&/g'
++ cat c:/jenkins/workspace/fiji-windows-core/jvm.cfg
+ eval java -Dpython.cachedir.skip=true -Xincgc -XX:PermSize=128m -Dplugins.dir=c:/jenkins/workspace/fiji-windows-core '-Djava.class.path=c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar\;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar\;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar\;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar\;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar\;c:/jenkins/workspace/fiji-windows-core/plugins/*.jar' -Dsun.java.command=Fiji -Dij.dir=c:/jenkins/workspace/fiji-windows-core -Dfiji.dir=c:/jenkins/workspace/fiji-windows-core -Dfiji.executable=ImageJ.sh -Dij.executable=ImageJ.sh imagej.build.MiniMaven -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1 -DartifactId=verbose=true install
++ java -Dpython.cachedir.skip=true -Xincgc -XX:PermSize=128m -Dplugins.dir=c:/jenkins/workspace/fiji-windows-core '-Djava.class.path=c:/jenkins/workspace/fiji-windows-core/jars/ij-core-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/ij-minimaven-2.0.0-beta-7.1.jar;c:/jenkins/workspace/fiji-windows-core/jars/javac-2.0.0-SNAPSHOT.jar;c:/jenkins/workspace/fiji-windows-core/jars/scijava-common-1.5.0.jar;c:/jenkins/workspace/fiji-windows-core/jars/sezpoz-1.9-imagej.jar;c:/jenkins/workspace/fiji-windows-core/plugins/*.jar' -Dsun.java.command=Fiji -Dij.dir=c:/jenkins/workspace/fiji-windows-core -Dfiji.dir=c:/jenkins/workspace/fiji-windows-core -Dfiji.executable=ImageJ.sh -Dij.executable=ImageJ.sh imagej.build.MiniMaven -Dimagej.app.directory=/c/jenkins/workspace/fiji-windows-core -Dminimaven.updateinterval=1 -DartifactId=verbose=true install
Looking at children of pom-fiji
Looking at children of pom-fiji-plugins
Compiling 27 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\fiji-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 22 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\pal-optimization
Compiling 180 files in C:\jenkins\workspace\fiji-windows-core\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 520 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\legacy-imglib1
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 121 files in C:\jenkins\workspace\fiji-windows-core\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 35 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\level_sets
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\3D_Blob_Segmentation
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\3D_Blob_Segmentation\src\main\java\ij3d\segmentation\Blob_Segmentation_in_3D.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\3D_Blob_Segmentation\src\main\java\ij3d\segmentation\Blob_Segmentation_in_3D.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 4 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\3D_Objects_Counter
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\3D_Objects_Counter\src\main\java\Utilities\Counter3D.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 3 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Algorithm_Launcher
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\Algorithm_Launcher\src\main\java\AlgorithmInfo.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 6 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\AnalyzeSkeleton_
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\AnalyzeSkeleton_\src\main\java\skeleton_analysis\AnalyzeSkeleton_.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 2 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Analyze_Reader_Writer
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Anisotropic_Diffusion_2D
Compiling 3 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Arrow_
Compiling 2 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Auto_Threshold
Compiling 8 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\BalloonSegmentation_
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\BalloonSegmentation_\src\main\java\BalloonSegmentation_.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 26 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\fiji-compat
Compiling 3 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\fiji-scripting
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 2 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\BeanShell_Interpreter
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\ij-core-2.0.0-beta-7.1.jar'
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\ij-minimaven-2.0.0-beta-7.1.jar'
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\jai_imageio-4.4.8.jar'
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Compiling 3 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Bug_Submitter
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Compiling 9 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\CLI_
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.
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\CPU_Meter
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Calculator_Plus
Compiling 2 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Clojure_Interpreter
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\Clojure_Interpreter\src\main\java\Clojure\Clojure_Interpreter.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Compiling 32 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Colocalisation_Analysis
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\Colocalisation_Analysis\src\main\java\results\SingleWindowDisplay.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Color_Histogram
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\Color_Histogram\src\main\java\ColorHistogram_.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 4 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Color_Inspector_3D
Note: C:\jenkins\workspace\fiji-windows-core\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.
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Colour_Deconvolution
Compiling 8 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\CorrectBleach_
Compiling 33 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Fiji_Plugins
C:\jenkins\workspace\fiji-windows-core\src-plugins\Fiji_Plugins\src\main\java\fiji\geom\Shape_Index_Map.java:17: warning: unmappable character for encoding Cp1252
* curvature scales,� Image Vision Comput, vol. 10, no. 8,
^
Note: C:\jenkins\workspace\fiji-windows-core\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.
Compiling 16 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\SPIM_Opener
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\SPIM_Opener\src\main\java\spimopener\GaussianStackFocuser.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Compiling 155 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\SPIM_Registration
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 59 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Stitching_
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 16 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Descriptor_based_registration
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\jai_imageio-1.0.1.jar'
Warning: deleting 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Warning: could not delete 'C:\jenkins\workspace\fiji-windows-core\jars\scijava-common-1.5.0.jar'
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Dichromacy_
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Differentials_
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Directionality_
Compiling 30 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\imageware
Compiling 5 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\wavelets
Compiling 31 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Extended_Depth_Field
Note: C:\jenkins\workspace\fiji-windows-core\src-plugins\Extended_Depth_Field\src\main\java\surfacemap\SurfaceMap3D.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 5 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Lasso_and_Blow_Tool
Compiling 1 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\Skeletonize3D_
Compiling 117 files in C:\jenkins\workspace\fiji-windows-core\src-plugins\VIB_
C:\jenkins\workspace\fiji-windows-core\src-plugins\VIB_\src\main\java\marchingcubes\ExportMesh_.java:35: cannot access mpicbg.imglib.type.numeric.RealType
class file for mpicbg.imglib.type.numeric.RealType not found
List mesh = triangulator.getTriangles(
^
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.
1 error
Exception in thread "main" imagej.build.minimaven.JavaCompiler$CompileError: Compile error: 1
at imagej.build.minimaven.JavaCompiler.call(JavaCompiler.java:83)
at imagej.build.minimaven.MavenProject.build(MavenProject.java:446)
at imagej.build.minimaven.MavenProject.build(MavenProject.java:377)
at imagej.build.minimaven.MavenProject.build(MavenProject.java:400)
at imagej.build.minimaven.MavenProject.build(MavenProject.java:377)
at imagej.build.minimaven.MavenProject.build(MavenProject.java:400)
at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:334)
at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:329)
at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:329)
at imagej.build.minimaven.MavenProject.buildAndInstall(MavenProject.java:290)
at imagej.build.MiniMaven.main(MiniMaven.java:144)
Build step 'Execute shell' marked build as failure
Build step 'Groovy Postbuild' marked build as failure
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