[ImageJ-builds] Build failed in Jenkins: fiji-core #478

Mon Aug 27 14:03:00 CDT 2012

See <https://qa.nest-initiative.org/job/fiji-core/478/changes>

Changes:

[iarganda] Weka Segmentation: added experimental max pooling methods.

[johannes.schindelin] Get rid of a lot of precompiled stuff

[johannes.schindelin] Clean up Fakefile

[johannes.schindelin] MiniMaven: heed the onlyNewer parameter of copyDependencies

[johannes.schindelin] Fiji Build (MiniMaven): make sure that IJ1 plugins are put into plugins/

[johannes.schindelin] Update .gitignore after recent cleanups

[johannes.schindelin] Woops. Put back a few files required for the TrakEM2 build

[ctrueden] Fix EOF newlines

[ctrueden] Remove unused loci_tools dependency

[ctrueden] Explicitly list Bio-Formats-related dependencies

[stephan.preibisch] Fixed nasty multi-threaded bug in content-based fusion

[stephan.preibisch] Debugging interval can be chosen

[stephan.preibisch] Saving as slices is now part of SPIM Registration, add an additional "z" tag for each filename index

[stephan.preibisch] Simplification, removed empty interface

[stephan.preibisch] Fixed some bugs that I missed

[stephan.preibisch] Fixed a bug in computing output image size when only one image is part of the collection

[johannes.schindelin] MiniMaven: fix NullPointerException

[jenkins] Soft-commit ImageJA

[johannes.schindelin] Bead-registration: add a main() method to make debugging easier

[johannes.schindelin] Bead registration: work around an unwelcome behavior of GenericDialog

[johannes.schindelin] Bead Registration: only record values when the dialog was not canceled

[johannes.schindelin] Make the debug helper for SPIM Registration more generic

[johannes.schindelin] Add a debug helper for filter plugins, too

[johannes.schindelin] bin/maven.sh: use maven 3.0.4 instead of 2.2.1

[stephan.preibisch] Removed unnecessary warnings

[iarganda] Weka Segmentation: update list of enabled features when setting an arbitrary feature stack, as pointed nicely out by Johannes Schindelin.

[iarganda] Weka Segmentation: set feature stacks to be updated during train and test while using an arbitrary feature stack array. Reported by Johannes Schindelin.

[johannes.schindelin] Update the scijava pom version to use

[stephan.preibisch] added new deconvolution to test

[johannes.schindelin] Fix two compiler warnings

[johannes.schindelin] Fiji Build: do not complain about using obsolete launcher anymore

[johannes.schindelin] Fiji Build: ensure ij.dir is set correctly

[johannes.schindelin] MiniMaven: write the manifest to target/classes/

[johannes.schindelin] MiniMaven: special-case the Fiji Updater

[johannes.schindelin] MiniMaven: fix compiler warnings

[johannes.schindelin] MiniMaven: make it an error when the parent POM could not be found

[johannes.schindelin] MiniMaven: fix borked upToDate() logic

[johannes.schindelin] MiniMaven: try to be gentle with invalid dependencies

[johannes.schindelin] MiniMaven: make sure that .pom *and* .jar are downloaded

[johannes.schindelin] MiniMaven: a TODO was squashed

[johannes.schindelin] MiniMaven: keep newlines in executed programs' output

[johannes.schindelin] Updater: add some functions to access the ImageJ Updater

[johannes.schindelin] Updater: add more functions to access the ImageJ Updater

[johannes.schindelin] Special-case the first ImageJ Updater run

[johannes.schindelin] Refactor the ImageJ Updater Adapter

[johannes.schindelin] Updater adapter: add a stderr-based user interface

[johannes.schindelin] Updater: also access ImageJ2's command-line Updater

[johannes.schindelin] Bug Submitter: use the new functions of the ImageJ Updater

[johannes.schindelin] Package Maker: use the new functions of the ImageJ Updater

[johannes.schindelin] Updater: show the status when accessing the ImageJ updater

[johannes.schindelin] Update Fiji: Use the ImageJ Updater

[johannes.schindelin] Complete the move of the Fiji Updater into ImageJ's code base

[johannes.schindelin] Update calculate-checksums.bsh to use the ImageJ Updater

[johannes.schindelin] Make sure the ImageJ updater finds its uploaders

[johannes.schindelin] Fiji Build: keep the version numbers for IJ2 and ImgLib2

[johannes.schindelin] Packager: in headless mode, do not try to use a graphical progress

[stephan.preibisch] Fixed a lot of bugs, works with timeseries

[stephan.preibisch] fixed a compile bug in deconvolution-fusion

[johannes.schindelin] Fix a couple of versions in the pom.xml files

[stephan.preibisch] Deconvolution works with multiple timepoints, and writes correctly

[johannes.schindelin] Fix a couple of dependency versions in the pom.xml files

[johannes.schindelin] ImageJ updater adapter: make sure to use the appropriate progress class

[johannes.schindelin] Fix the previous commit

[johannes.schindelin] Bug Submitter: avoid stack overflow

[johannes.schindelin] ImageJ updater adapter: fix the call to getLocalFilename()

[ctrueden] Stitcher: add options to invert X and/or Y axes

[ctrueden] Update Bio-Formats submodule to latest HEAD

[ctrueden] Update ImageJ2 & ImgLib submodules to latest HEAD

[johannes.schindelin] Commit almost up-to-date ImageJ2 submodule

[johannes.schindelin] Upgrade TrackMate to JFreeChart 1.0.14

[stephan.preibisch] Multi-threaded non-convolution parts

[stephan.preibisch] Fixes in the UI class

[stephan.preibisch] Small fix in how to call deconvolution

[stephan.preibisch] Undone the speed-up

[stephan.preibisch] Updated GUI to ask for blockSize, where to compute and removed old questions that do not apply anymore

[stephan.preibisch] Removed import

[ctrueden] Add Coordinate#getVersion() for resolved version

[ctrueden] Fix bug when resolving dependency versions

[johannes.schindelin] Add a Beanshell to find .jar classes containing a given class

[johannes.schindelin] Fiji Updater: be more quiet when ij.IJ was not found

[johannes.schindelin] Fiji Updater: do not even try to access ij.IJ from the command-line

[stephan.preibisch] Generalizing convolution so that it can execute different ways to convolve images

[stephan.preibisch] Can compute the convolution in blocks to use less memory or cuda

[stephan.preibisch] fixed bugs in the blocking, works now

[stephan.preibisch] Deconvolution works as chunk or in blocks, ready for CUDA

[stephan.preibisch] cuda usage is assigned, more debug for the paramters involved

[stephan.preibisch] removed comments

[stephan.preibisch] Added debug output

[amatf] cuda convolution test

[amatf] added the interface for calling CUDA

[johannes.schindelin] build-launcher (linux32): make sure a 32-bit executable is built

[amatf] deconvolution seems to work, blocks still have a bug or two

[stephan.preibisch] fixed fiji for now

[stephan.preibisch] fixed bug in LRFFT

[johannes.schindelin] Update ImgLib (1!) as required by SPIM Registration

[stephan.preibisch] Fixed more bugs in the block deconvolution

[stephan.preibisch] working on fast copy method for 3d

[stephan.preibisch] fixed bug in copy3d

[stephan.preibisch] updated the copy and paste block calls

[ctrueden] Add simple script for Rootbeer-izing ImageJ

[stephan.preibisch] Modified PSF extraction

[iarganda] Weka Segmentation: fixed small bug in method randIndex and commented getRandIndexStats methods better. The Rand index is calculated in an asymmetric way, pruning the zero component of the ground truth. This means background pixels of the ground truth do not compute in the Rand index. This is the most robust way of doing it, since using a symmetric approach would mean that background pixels do not compute at all (a complete zero prediction would have zero error).

[jeanyves.tinevez] TrackMate_: add a logger that outputs to IJ log window

[jeanyves.tinevez] TrackMate_: ISBIChallengeExporter can be called from a script

[gregory] Made readme more github-friendly.

[gregory] Fixed the readme markup.

[ctrueden] README: make authors a bulleted list

[johannes.schindelin] Fiji Updater: try harder to run ImageJ's updater

[johannes.schindelin] Fiji Updater: hard-code a more current remote ImageJ2 updater version

[johannes.schindelin] Fiji Updater: fix tyop

[johannes.schindelin] Jama is not really a child project of Fiji...

[johannes.schindelin] Remove loci_tools.jar from the Fakefile

[johannes.schindelin] Remove unused lines from the Fakefile

[johannes.schindelin] Allow MiniMaven to run within Eclipse

[johannes.schindelin] MiniMaven: add two API methods to access the packaging and directory fields

[johannes.schindelin] MiniMaven: make verbose mode more verbose

[johannes.schindelin] MiniMaven: special-case Bio-Formats

[johannes.schindelin] Support aggregator .pom files in the Fiji Build

[johannes.schindelin] Fiji Build (MiniMaven): improve check for IJ1 plugins

[johannes.schindelin] Let src-plugins/pom.xml alone specify which artifacts to build

[johannes.schindelin] Prepare Build.sh for a versioned fake.jar file

[johannes.schindelin] Prepare ImageJ.sh for a versioned fake.jar file

[johannes.schindelin] Build versioned .jar files by default

[johannes.schindelin] Fiji Build: accept versioned .jar names as targets

[johannes.schindelin] Fiji Build (MiniMaven): support command-line verbose settings

[johannes.schindelin] Fiji Build (MiniMaven): Clean also the copies of the build artifacts

[johannes.schindelin] Fiji Build: make sure that Fiji_Updater.jar is really unversioned

[johannes.schindelin] Volume Viewer: add a plugins.config file

[johannes.schindelin] download-launchers: use versioned filename for ij-launcher.jar

[johannes.schindelin] build-launcher: use versioned filename for ij-launcher.jar

[johannes.schindelin] .gitignore: ignore versioned instead of unversioned .jar files

[johannes.schindelin] MiniMaven: heed update-interval also for version ranges

[johannes.schindelin] MiniMaven: when given a version range, look for new versions

[johannes.schindelin] Require the newest scijava pom

[johannes.schindelin] Add missing entries to .gitignore

[johannes.schindelin] Build.sh: update the dependencies of fake before building it

[johannes.schindelin] wip

------------------------------------------
Started by user Johannes Schindelin
Building remotely on fc-16-i386-1 in workspace <https://qa.nest-initiative.org/job/fiji-core/ws/>
Checkout:fiji-core / <https://qa.nest-initiative.org/job/fiji-core/ws/> - hudson.remoting.Channel at 5ffc6345:fc-16-i386-1
Using strategy: Default
Last Built Revision: Revision e925af156877996069588c910b920d5b1b75daa2 (origin/master)
Fetching changes from 1 remote Git repository
Fetching upstream changes from git://github.com/fiji/fiji
Commencing build of Revision 16af5bfab5e3af6580e441348a5886349ef0e734 (origin/master2)
Checking out Revision 16af5bfab5e3af6580e441348a5886349ef0e734 (origin/master2)
Cleaning workspace
Resetting working tree
Deleting old artifacts from #476
[fiji-core] $ /bin/bash /tmp/hudson8350160441524216379.sh
+ ./Build.sh -Dminimaven.updateinterval=1 -- verbose=true
Exception in thread "main" java.lang.RuntimeException: Parent not found: org.scijava/pom-scijava-1.19 (please call MiniMaven's 'download'
	at fiji.build.minimaven.BuildEnvironment.parse(BuildEnvironment.java:175)
	at fiji.build.minimaven.BuildEnvironment.parse(BuildEnvironment.java:100)
	at fiji.build.MiniMaven.main(MiniMaven.java:47)
Could not build Fiji Build
Build step 'Execute shell' marked build as failure
Archiving artifacts