Source: biojava4-live Version: 4.2.4+dfsg-1 Severity: serious Tags: stretch sid User: debian...@lists.debian.org Usertags: qa-ftbfs-20161219 qa-ftbfs Justification: FTBFS on amd64
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<BUILDDIR>>/biojava4-live-4.2.4+dfsg' > cd biojava-jcolorbrewer && ant jar > Buildfile: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-jcolorbrewer/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-jcolorbrewer/classes > [mkdir] Created dir: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-jcolorbrewer/build.xml:76: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 9 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-jcolorbrewer/classes > [javac] Note: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-jcolorbrewer/src/main/java/org/jcolorbrewer/ui/ColorPaletteChooserDialog.java > uses or overrides a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [copy] Warning: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-jcolorbrewer/src/main/resources > does not exist. > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-jcolorbrewer.jar > > BUILD SUCCESSFUL > Total time: 1 second > cd biojava-forester && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-forester/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-forester/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-forester/build.xml:76: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 359 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-forester/classes > [javac] Note: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java > uses or overrides a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [copy] Warning: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-forester/src/main/resources > does not exist. > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-forester.jar > > BUILD SUCCESSFUL > Total time: 4 seconds > cd biojava-core && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-core/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-core/classes > [javac] /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-core/build.xml:76: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 176 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-core/classes > [javac] Note: Some input files use unchecked or unsafe operations. > [javac] Note: Recompile with -Xlint:unchecked for details. > [copy] Copying 24 files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-core/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-core.jar > > BUILD SUCCESSFUL > Total time: 2 seconds > cd biojava-phylo && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-phylo/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-phylo/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-phylo/build.xml:76: warning: > 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set > to false for repeatable builds > [javac] Compiling 8 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-phylo/classes > [copy] Copying 2 files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-phylo/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-phylo.jar > > BUILD SUCCESSFUL > Total time: 0 seconds > cd biojava-alignment && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-alignment/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-alignment/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-alignment/build.xml:76: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 45 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-alignment/classes > [copy] Copying 1 file to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-alignment/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-alignment.jar > > BUILD SUCCESSFUL > Total time: 1 second > cd biojava-aa-prop && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-aa-prop/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-aa-prop/build.xml:76: warning: > 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set > to false for repeatable builds > [javac] Compiling 32 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes > [javac] Creating empty > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/xml/package-info.class > [javac] Creating empty > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/package-info.class > [javac] Creating empty > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/profeat/convertor/package-info.class > [javac] Creating empty > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes/org/biojava/nbio/aaproperties/package-info.class > [copy] Copying 11 files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-aa-prop/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-aa-prop.jar > > BUILD SUCCESSFUL > Total time: 1 second > cd biojava-genome && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-genome/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-genome/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-genome/build.xml:76: warning: > 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set > to false for repeatable builds > [javac] Compiling 30 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-genome/classes > [javac] Note: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java > uses unchecked or unsafe operations. > [javac] Note: Recompile with -Xlint:unchecked for details. > [copy] Copying 1 file to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-genome/classes > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-genome.jar > > BUILD SUCCESSFUL > Total time: 1 second > cd biojava-sequencing && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-sequencing/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-sequencing/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-sequencing/build.xml:76: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 19 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-sequencing/classes > [javac] Creating empty > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-sequencing/classes/org/biojava/nbio/sequencing/io/fastq/package-info.class > [copy] Warning: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-sequencing/src/main/resources > does not exist. > > jar: > [jar] Building jar: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/dist/biojava4-sequencing.jar > > BUILD SUCCESSFUL > Total time: 0 seconds > cd biojava-structure && ant jar > Buildfile: /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/build.xml > > compile: > [mkdir] Created dir: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-structure/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/build.xml:76: > warning: 'includeantruntime' was not set, defaulting to > build.sysclasspath=last; set to false for repeatable builds > [javac] Compiling 482 source files to > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/build/biojava4-structure/classes > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:27: > error: package org.jgrapht does not exist > [javac] import org.jgrapht.UndirectedGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:28: > error: package org.jgrapht.alg does not exist > [javac] import org.jgrapht.alg.ConnectivityInspector; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:29: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.DefaultEdge; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:30: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.UndirectedSubgraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:467: > error: cannot find symbol > [javac] private static boolean > isConnectedGraph(UndirectedGraph<Integer, DefaultEdge> graph) { > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:467: > error: cannot find symbol > [javac] private static boolean > isConnectedGraph(UndirectedGraph<Integer, DefaultEdge> graph) { > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:25: > error: package org.jgrapht does not exist > [javac] import org.jgrapht.UndirectedGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:26: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.DefaultEdge; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:27: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.SimpleGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:46: > error: cannot find symbol > [javac] public UndirectedGraph<Integer, DefaultEdge> getProteinGraph() { > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:46: > error: cannot find symbol > [javac] public UndirectedGraph<Integer, DefaultEdge> getProteinGraph() { > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:48: > error: package org.jgrapht does not exist > [javac] import org.jgrapht.UndirectedGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:49: > error: package org.jgrapht.alg does not exist > [javac] import org.jgrapht.alg.ConnectivityInspector; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:50: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.DefaultEdge; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:51: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.SimpleGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:79: > error: cannot find symbol > [javac] private UndirectedGraph<Integer, DefaultEdge> alignGraph; // > cumulative > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:79: > error: cannot find symbol > [javac] private UndirectedGraph<Integer, DefaultEdge> alignGraph; // > cumulative > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:31: > error: package org.jgrapht does not exist > [javac] import org.jgrapht.UndirectedGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:32: > error: package org.jgrapht.alg does not exist > [javac] import org.jgrapht.alg.ConnectivityInspector; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:33: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.DefaultEdge; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:37: > error: package org.jgrapht does not exist > [javac] import org.jgrapht.UndirectedGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:38: > error: package org.jgrapht.alg does not exist > [javac] import org.jgrapht.alg.ConnectivityInspector; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:39: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.DefaultEdge; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:65: > error: package org.jgrapht does not exist > [javac] import org.jgrapht.UndirectedGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:66: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.DefaultEdge; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:67: > error: package org.jgrapht.graph does not exist > [javac] import org.jgrapht.graph.SimpleGraph; > [javac] ^ > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:477: > error: cannot find symbol > [javac] public static UndirectedGraph<Integer, DefaultEdge> > buildSymmetryGraph( > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class SymmetryTools > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:477: > error: cannot find symbol > [javac] public static UndirectedGraph<Integer, DefaultEdge> > buildSymmetryGraph( > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class SymmetryTools > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:399: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = > subunitGraph.getProteinGraph(); > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:399: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = > subunitGraph.getProteinGraph(); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:437: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> > subGraph = new UndirectedSubgraph<Integer, DefaultEdge>(graph, new > HashSet<Integer>(subSet), null); > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:437: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> > subGraph = new UndirectedSubgraph<Integer, DefaultEdge>(graph, new > HashSet<Integer>(subSet), null); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:437: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> > subGraph = new UndirectedSubgraph<Integer, DefaultEdge>(graph, new > HashSet<Integer>(subSet), null); > [javac] > ^ > [javac] symbol: class UndirectedSubgraph > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:437: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> > subGraph = new UndirectedSubgraph<Integer, DefaultEdge>(graph, new > HashSet<Integer>(subSet), null); > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:468: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>(graph); > [javac] ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:468: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>(graph); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:468: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>(graph); > [javac] > ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java:468: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>(graph); > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class QuatSymmetryDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:50: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class); > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:50: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:50: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class); > [javac] ^ > [javac] symbol: class SimpleGraph > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:50: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class); > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SubunitGraph.java:50: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>(DefaultEdge.class); > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class SubunitGraph > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:92: > error: cannot find symbol > [javac] alignGraph = new SimpleGraph<Integer, > DefaultEdge>(DefaultEdge.class); > [javac] ^ > [javac] symbol: class SimpleGraph > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:92: > error: cannot find symbol > [javac] alignGraph = new SimpleGraph<Integer, > DefaultEdge>(DefaultEdge.class); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:92: > error: cannot find symbol > [javac] alignGraph = new SimpleGraph<Integer, > DefaultEdge>(DefaultEdge.class); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:233: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:233: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:233: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] > ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java:233: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class CeSymmIterative > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:53: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = > SymmetryTools > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class GraphComponentOrderDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:53: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = > SymmetryTools > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class GraphComponentOrderDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:57: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > [javac] ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class GraphComponentOrderDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:57: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class GraphComponentOrderDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:58: > error: cannot find symbol > [javac] new ConnectivityInspector<Integer, > DefaultEdge>(graph); > [javac] ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class GraphComponentOrderDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java:58: > error: cannot find symbol > [javac] new ConnectivityInspector<Integer, > DefaultEdge>(graph); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class GraphComponentOrderDetector > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:62: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = > SymmetryTools > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class GraphComponentRefiner > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:62: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = > SymmetryTools > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class GraphComponentRefiner > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:66: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class GraphComponentRefiner > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:66: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class GraphComponentRefiner > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:66: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] > ^ > [javac] symbol: class ConnectivityInspector > [javac] location: class GraphComponentRefiner > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java:66: > error: cannot find symbol > [javac] ConnectivityInspector<Integer, DefaultEdge> inspector = > new ConnectivityInspector<Integer, DefaultEdge>( > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class GraphComponentRefiner > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:480: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class UndirectedGraph > [javac] location: class SymmetryTools > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:480: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class SymmetryTools > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:480: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>( > [javac] ^ > [javac] symbol: class SimpleGraph > [javac] location: class SymmetryTools > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:480: > error: cannot find symbol > [javac] UndirectedGraph<Integer, DefaultEdge> graph = new > SimpleGraph<Integer, DefaultEdge>( > [javac] > ^ > [javac] symbol: class DefaultEdge > [javac] location: class SymmetryTools > [javac] > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java:481: > error: cannot find symbol > [javac] DefaultEdge.class); > [javac] ^ > [javac] symbol: class DefaultEdge > [javac] location: class SymmetryTools > [javac] Note: Some input files use or override a deprecated API. > [javac] Note: Recompile with -Xlint:deprecation for details. > [javac] Note: > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MetalBondConsumer.java > uses unchecked or unsafe operations. > [javac] Note: Recompile with -Xlint:unchecked for details. > [javac] 67 errors > > BUILD FAILED > /<<BUILDDIR>>/biojava4-live-4.2.4+dfsg/biojava-structure/build.xml:76: > Compile failed; see the compiler error output for details. > > Total time: 3 seconds > debian/rules:34: recipe for target 'override_dh_auto_build' failed > make[1]: *** [override_dh_auto_build] Error 1 The full build log is available from: http://aws-logs.debian.net/2016/12/19/biojava4-live_4.2.4+dfsg-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.