[ImageJ-builds] Build failed in Jenkins: TrakEM2 #81
jenkins at imagej.net
jenkins at imagej.net
Thu Sep 3 17:29:02 CDT 2015
See <http://jenkins.imagej.net/job/TrakEM2/81/changes>
Changes:
[Stephan Saalfeld] included match intensities plugin, build with SNAPSHOTS for testing
[Stephan Saalfeld] Working version without multi-threading and bureaucrats
[Stephan Saalfeld] put match intensities commands into workers to block input accordingly
[Stephan Saalfeld] added multi-threading for coefficients matching
[Stephan Saalfeld] pom-trakem2-1.4.0
------------------------------------------
Started by an SCM change
Started by an SCM change
Building on master in workspace <http://jenkins.imagej.net/job/TrakEM2/ws/>
> git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
> git config remote.origin.url git://github.com/trakem2/TrakEM2 # timeout=10
Fetching upstream changes from git://github.com/trakem2/TrakEM2
> git --version # timeout=10
> git -c core.askpass=true fetch --tags --progress git://github.com/trakem2/TrakEM2 +refs/heads/*:refs/remotes/origin/*
> git rev-parse origin/master^{commit} # timeout=10
Checking out Revision 11a1f44c75c7b9afb4a2b85507671d7b24df5490 (origin/master)
> git config core.sparsecheckout # timeout=10
> git checkout -f 11a1f44c75c7b9afb4a2b85507671d7b24df5490
> git rev-list 4cf79524ef725cfe4ba87b9956933ac7beeb08af # timeout=10
> git tag -a -f -m Jenkins Build #81 jenkins-TrakEM2-81 # timeout=10
[workspace] $ /bin/sh -xe /tmp/hudson5567972735141014361.sh
+ git clean -dfx
[workspace] $ /bin/sh -xe /tmp/hudson2028503552973925628.sh
+ mvn -U -Pdeploy-to-imagej deploy
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] Aggregator project for Albert Cardona's TrakEM2 software suite
[INFO] plugins/TrakEM2_.jar
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Aggregator project for Albert Cardona's TrakEM2 software suite 1.4.0
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ pom-trakem2 ---
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO] Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO] Adding ignore: com/kenai/constantine/*
[INFO] Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO] Adding ignore: jnr/ffi/*
[INFO] Adding ignorable dependency: null:VIB-lib:null
[INFO] Adding ignore: javax/media/j3d/
[INFO] Adding ignorable dependency: null:j3d-core:null
[INFO] Adding ignore: javax/media/j3d/
[INFO] Adding ignorable dependency: null:joda-time:null
[INFO] Adding ignore: *
[INFO] Adding ignorable dependency: null:slf4j-log4j12:null
[INFO] Adding ignore: org/slf4j/impl/*
[INFO] Adding ignorable dependency: batik:batik:null
[INFO] Adding ignore: *
[INFO] Adding ignorable dependency: jama:jama:null
[INFO] Adding ignore: Jama/*
[INFO] Adding ignorable dependency: com.sun:tools:null
[INFO] Adding ignore: *
[INFO]
[INFO] --- build-helper-maven-plugin:1.9.1:regex-property (sanitize-version) @ pom-trakem2 ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ pom-trakem2 ---
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/TrakEM2/workspace && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/TrakEM2/workspace
[INFO] Storing buildNumber: 11a1f44c75c7b9afb4a2b85507671d7b24df5490 at timestamp: 1441319325293
[WARNING] Cannot get the branch information from the git repository:
Detecting the current branch failed: fatal: ref HEAD is not a symbolic ref
[INFO] Executing: /bin/sh -c cd /data/devel/jenkins/jobs/TrakEM2/workspace && git rev-parse --verify HEAD
[INFO] Working directory: /data/devel/jenkins/jobs/TrakEM2/workspace
[INFO] Storing buildScmBranch: UNKNOWN
[INFO]
[INFO] --- scijava-maven-plugin:0.5.0:set-rootdir (set-rootdir) @ pom-trakem2 ---
[INFO] Setting rootdir: /data/devel/jenkins/jobs/TrakEM2/workspace
[INFO]
[INFO] --- maven-source-plugin:2.3:jar-no-fork (default) @ pom-trakem2 ---
[INFO]
[INFO] --- maven-source-plugin:2.3:jar-no-fork (attach-sources) @ pom-trakem2 ---
[INFO]
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ pom-trakem2 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO]
[INFO] --- maven-install-plugin:2.5.1:install (default-install) @ pom-trakem2 ---
[INFO] Installing /data/devel/jenkins/jobs/TrakEM2/workspace/pom.xml to /var/lib/jenkins/.m2/repository/sc/fiji/pom-trakem2/1.4.0/pom-trakem2-1.4.0.pom
[INFO]
[INFO] --- imagej-maven-plugin:0.6.0:copy-jars (copy-jars) @ pom-trakem2 ---
[INFO]
[INFO] --- maven-deploy-plugin:2.8.1:deploy (default-deploy) @ pom-trakem2 ---
Uploading: dav:http://maven.imagej.net/content/repositories/releases/sc/fiji/pom-trakem2/1.4.0/pom-trakem2-1.4.0.pom
Sep 3, 2015 5:28:46 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
4/5 KB
5/5 KB
Sep 3, 2015 5:28:46 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
9/5 KB
10/5 KB
Sep 3, 2015 5:28:46 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Sep 3, 2015 5:28:46 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Sep 3, 2015 5:28:46 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Sep 3, 2015 5:28:46 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Uploaded: dav:http://maven.imagej.net/content/repositories/releases/sc/fiji/pom-trakem2/1.4.0/pom-trakem2-1.4.0.pom (10 KB at 28.1 KB/sec)
Downloading: http://maven.imagej.net/content/repositories/releases/sc/fiji/pom-trakem2/maven-metadata.xml
484/484 B
Downloaded: http://maven.imagej.net/content/repositories/releases/sc/fiji/pom-trakem2/maven-metadata.xml (484 B at 1.9 KB/sec)
Uploading: http://maven.imagej.net/content/repositories/releases/sc/fiji/pom-trakem2/maven-metadata.xml
Sep 3, 2015 5:28:47 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
515/515 B
Sep 3, 2015 5:28:47 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
1030/515 B
Sep 3, 2015 5:28:47 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Sep 3, 2015 5:28:47 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Sep 3, 2015 5:28:47 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Sep 3, 2015 5:28:47 PM org.apache.commons.httpclient.auth.AuthChallengeProcessor selectAuthScheme
INFO: basic authentication scheme selected
Uploaded: http://maven.imagej.net/content/repositories/releases/sc/fiji/pom-trakem2/maven-metadata.xml (2 KB at 13.6 KB/sec)
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building plugins/TrakEM2_.jar 1.0g
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.3.1:enforce (enforce-rules) @ TrakEM2_ ---
Downloading: http://maven.imagej.net/content/groups/public/com/sun/tools/1.4.2/tools-1.4.2.pom
Downloading: http://repo.maven.apache.org/maven2/com/sun/tools/1.4.2/tools-1.4.2.pom
[INFO] Adding ignorable dependency: null:jcodings:null
[INFO] Adding ignore: org/jcodings/*
[INFO] Adding ignorable dependency: null:jnr-constants:null
[INFO] Adding ignore: com/kenai/constantine/*
[INFO] Adding ignore: jnr/constants/*
[INFO] Adding ignorable dependency: null:jnr-ffi:null
[INFO] Adding ignore: jnr/ffi/*
[INFO] Adding ignorable dependency: null:VIB-lib:null
[INFO] Adding ignore: javax/media/j3d/
[INFO] Adding ignorable dependency: null:j3d-core:null
[INFO] Adding ignore: javax/media/j3d/
[INFO] Adding ignorable dependency: null:joda-time:null
[INFO] Adding ignore: *
[INFO] Adding ignorable dependency: null:slf4j-log4j12:null
[INFO] Adding ignore: org/slf4j/impl/*
[INFO] Adding ignorable dependency: batik:batik:null
[INFO] Adding ignore: *
[INFO] Adding ignorable dependency: jama:jama:null
[INFO] Adding ignore: Jama/*
[INFO] Adding ignorable dependency: com.sun:tools:null
[INFO] Adding ignore: *
[INFO]
[INFO] --- build-helper-maven-plugin:1.9.1:regex-property (sanitize-version) @ TrakEM2_ ---
[INFO] No match to regex '^([0-9]+)\.([0-9]+)\.([0-9]+).*$' found in '1.0g'. The initial value '1.0g' is left as-is...
[INFO]
[INFO] --- buildnumber-maven-plugin:1.3:create (default) @ TrakEM2_ ---
[INFO]
[INFO] --- scijava-maven-plugin:0.5.0:set-rootdir (set-rootdir) @ TrakEM2_ ---
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ TrakEM2_ ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 11 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ TrakEM2_ ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 245 source files to /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/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.
[WARNING] Note: Some input files use unchecked or unsafe operations.
[WARNING] Note: Recompile with -Xlint:unchecked for details.
[INFO] 4 warnings
[INFO] -------------------------------------------------------------
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/src/main/java/ini/trakem2/persistence/FSLoader.java:[3087,83] incompatible types; inferred type argument(s) java.lang.Object do not conform to bounds of type variable(s) T
found : <T>net.imglib2.img.imageplus.ImagePlusImg<T,?>
required: java.lang.Object
[ERROR] /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/src/main/java/org/janelia/intensity/MatchIntensities.java:[341,28] incompatible types; inferred type argument(s) java.lang.Object do not conform to bounds of type variable(s) M
found : <M>void
required: void
[ERROR] /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/src/main/java/org/janelia/intensity/LinearIntensityMap.java:[135,94] inconvertible types
found : net.imglib2.RandomAccessibleInterval<S>
required: net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.ARGBType>
[INFO] 3 errors
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Aggregator project for Albert Cardona's TrakEM2 software suite SUCCESS [3.805s]
[INFO] plugins/TrakEM2_.jar .............................. FAILURE [14.924s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 19.624s
[INFO] Finished at: Thu Sep 03 17:29:02 CDT 2015
[INFO] Final Memory: 42M/513M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project TrakEM2_: Compilation failure: Compilation failure:
[ERROR] /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/src/main/java/ini/trakem2/persistence/FSLoader.java:[3087,83] incompatible types; inferred type argument(s) java.lang.Object do not conform to bounds of type variable(s) T
[ERROR] found : <T>net.imglib2.img.imageplus.ImagePlusImg<T,?>
[ERROR] required: java.lang.Object
[ERROR] /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/src/main/java/org/janelia/intensity/MatchIntensities.java:[341,28] incompatible types; inferred type argument(s) java.lang.Object do not conform to bounds of type variable(s) M
[ERROR] found : <M>void
[ERROR] required: void
[ERROR] /data/devel/jenkins/jobs/TrakEM2/workspace/TrakEM2_/src/main/java/org/janelia/intensity/LinearIntensityMap.java:[135,94] inconvertible types
[ERROR] found : net.imglib2.RandomAccessibleInterval<S>
[ERROR] required: net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.ARGBType>
[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 :TrakEM2_
Build step 'Execute shell' marked build as failure
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