[Debian-med-packaging] Bug#848768: biojava4-live: FTBFS: [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
Lucas Nussbaum
lucas at debian.org
Mon Dec 19 21:08:48 UTC 2016
Source: biojava4-live
Version: 4.2.4+dfsg-1
Severity: serious
Tags: stretch sid
User: debian-qa at 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.
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