gistfile1.txt

(base) pietzsch@tomancak-mac-26:~/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm (d39889d*)$ cat build.log                                             # 0 [22:48:51]
[INFO] Scanning for projects...
[INFO]
[INFO] -------------------< net.imglib2:imglib2-algorithm >--------------------
[INFO] Building ImgLib2 Algorithms 0.11.2
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-rules) @ imglib2-algorithm ---
[INFO] Skipping Rule Enforcement.
[INFO]
[INFO] --- build-helper-maven-plugin:3.0.0:regex-property (sanitize-version) @ imglib2-algorithm ---
[INFO]
[INFO] --- buildnumber-maven-plugin:1.4:create (default) @ imglib2-algorithm ---
[INFO] Executing: /bin/sh -c cd '/Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm
[INFO] Storing buildNumber: d39889dbfaf6b3ad656e1387b0adbb28d8259c55 at timestamp: 1586261332185
[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 '/Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm
[INFO] Storing buildScmBranch: UNKNOWN
[INFO]
[INFO] --- scijava-maven-plugin:1.1.0:set-rootdir (set-rootdir) @ imglib2-algorithm ---
[INFO] Setting rootdir: /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm
[INFO]
[INFO] --- jacoco-maven-plugin:0.8.4:prepare-agent (jacoco-initialize) @ imglib2-algorithm ---
[INFO] argLine set to -javaagent:/Users/pietzsch/.m2/repository/org/jacoco/org.jacoco.agent/0.8.4/org.jacoco.agent-0.8.4-runtime.jar=destfile=/Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/target/jacoco.exec
[INFO]
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ imglib2-algorithm ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ imglib2-algorithm ---
[INFO] Compiling 278 source files to /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/target/classes
[INFO] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/labeling/AllConnectedComponents.java: Some input files use or override a deprecated API.
[INFO] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/labeling/AllConnectedComponents.java: Recompile with -Xlint:deprecation for details.
[INFO] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/convolution/Convolution.java: Some input files use unchecked or unsafe operations.
[INFO] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/convolution/Convolution.java: Recompile with -Xlint:unchecked for details.
[INFO] Some messages have been simplified; recompile with -Xdiags:verbose to get full output
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[37,25] package org.ojalgo.access does not exist
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[51,72] cannot find symbol
  symbol: class Access2D
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[51,100] package Access2D does not exist
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSquare.java:[64,47] no suitable method found for make(net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T>,boolean)
    method org.ojalgo.matrix.decomposition.MatrixDecomposition.Factory.make(int,int) is not applicable
      (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to int)
    method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(int,boolean) is not applicable
      (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to int)
    method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(org.ojalgo.structure.Structure2D,boolean) is not applicable
      (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to org.ojalgo.structure.Structure2D)
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSquare.java:[71,43] incompatible types: net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to org.ojalgo.structure.Access2D.Collectable<java.lang.Double,? super org.ojalgo.matrix.store.PhysicalStore<java.lang.Double>>
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSymmetric.java:[64,47] no suitable method found for make(net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T>,boolean)
    method org.ojalgo.matrix.decomposition.MatrixDecomposition.Factory.make(int,int) is not applicable
      (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to int)
    method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(int,boolean) is not applicable
      (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to int)
    method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(org.ojalgo.structure.Structure2D,boolean) is not applicable
      (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to org.ojalgo.structure.Structure2D)
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSymmetric.java:[71,39] incompatible types: net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to org.ojalgo.structure.Access2D.Collectable<java.lang.Double,? super org.ojalgo.matrix.store.PhysicalStore<java.lang.Double>>
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[87,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[93,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[99,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[110,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[121,9] method does not override or implement a method from a supertype
[INFO] 12 errors
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  3.068 s
[INFO] Finished at: 2020-04-07T14:08:54+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project imglib2-algorithm: Compilation failure: Compilation failure:
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[37,25] package org.ojalgo.access does not exist
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[51,72] cannot find symbol
[ERROR]   symbol: class Access2D
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[51,100] package Access2D does not exist
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSquare.java:[64,47] no suitable method found for make(net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T>,boolean)
[ERROR]     method org.ojalgo.matrix.decomposition.MatrixDecomposition.Factory.make(int,int) is not applicable
[ERROR]       (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to int)
[ERROR]     method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(int,boolean) is not applicable
[ERROR]       (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to int)
[ERROR]     method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(org.ojalgo.structure.Structure2D,boolean) is not applicable
[ERROR]       (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to org.ojalgo.structure.Structure2D)
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSquare.java:[71,43] incompatible types: net.imglib2.algorithm.linalg.matrix.RealCompositeSquareMatrix<T> cannot be converted to org.ojalgo.structure.Access2D.Collectable<java.lang.Double,? super org.ojalgo.matrix.store.PhysicalStore<java.lang.Double>>
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSymmetric.java:[64,47] no suitable method found for make(net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T>,boolean)
[ERROR]     method org.ojalgo.matrix.decomposition.MatrixDecomposition.Factory.make(int,int) is not applicable
[ERROR]       (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to int)
[ERROR]     method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(int,boolean) is not applicable
[ERROR]       (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to int)
[ERROR]     method org.ojalgo.matrix.decomposition.Eigenvalue.Factory.make(org.ojalgo.structure.Structure2D,boolean) is not applicable
[ERROR]       (argument mismatch; net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to org.ojalgo.structure.Structure2D)
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/eigen/EigenValuesSymmetric.java:[71,39] incompatible types: net.imglib2.algorithm.linalg.matrix.RealCompositeSymmetricMatrix<T> cannot be converted to org.ojalgo.structure.Access2D.Collectable<java.lang.Double,? super org.ojalgo.matrix.store.PhysicalStore<java.lang.Double>>
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[87,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[93,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[99,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[110,9] method does not override or implement a method from a supertype
[ERROR] /Users/pietzsch/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm/src/main/java/net/imglib2/algorithm/linalg/matrix/RealCompositeMatrix.java:[121,9] method does not override or implement a method from a supertype
[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
(base) pietzsch@tomancak-mac-26:~/workspace/fiji/fiji/melting-pot/net.imglib2/imglib2-algorithm (d39889d*)$                                                           # 0 [22:49:37]