Package: src:biojava4-live; Maintainer for src:biojava4-live is Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>;
Reported by: Lucas Nussbaum <lucas@debian.org>
Date: Mon, 19 Dec 2016 21:26:15 UTC
Severity: serious
Tags: sid, stretch
Found in version biojava4-live/4.2.4+dfsg-1
Fixed in version biojava4-live/4.2.4+dfsg-2
Done: Olivier Sallou <osallou@debian.org>
Bug is archived. No further changes may be made.
View this report as an mbox folder, status mbox, maintainer mbox
Report forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#848768; Package src:biojava4-live.
(Mon, 19 Dec 2016 21:26:18 GMT) (full text, mbox, link).
Acknowledgement sent
to Lucas Nussbaum <lucas@debian.org>:
New Bug report received and forwarded. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Mon, 19 Dec 2016 21:26:18 GMT) (full text, mbox, link).
Message #5 received at submit@bugs.debian.org (full text, mbox, reply):
Source: biojava4-live
Version: 4.2.4+dfsg-1
Severity: serious
Tags: stretch sid
User: debian-qa@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.
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#848768; Package src:biojava4-live.
(Tue, 20 Dec 2016 07:39:07 GMT) (full text, mbox, link).
Acknowledgement sent
to Andreas Tille <tille@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Tue, 20 Dec 2016 07:39:07 GMT) (full text, mbox, link).
Message #10 received at 848768@bugs.debian.org (full text, mbox, reply):
Hi Olivier and Ximin,
I stripped the quote of the build log below but to me it seems to be
related to the jmol upgrade.
Any help to get this fixed would be really welcome.
Kind regards
Andreas.
On Mon, Dec 19, 2016 at 10:08:48PM +0100, Lucas Nussbaum wrote:
> Source: biojava4-live
> Version: 4.2.4+dfsg-1
> Severity: serious
> Tags: stretch sid
> User: debian-qa@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.
> ...
> > [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
--
http://fam-tille.de
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#848768; Package src:biojava4-live.
(Tue, 20 Dec 2016 07:57:06 GMT) (full text, mbox, link).
Acknowledgement sent
to olivier sallou <olivier.sallou@gmail.com>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Tue, 20 Dec 2016 07:57:06 GMT) (full text, mbox, link).
Message #15 received at 848768@bugs.debian.org (full text, mbox, reply):
[Message part 1 (text/plain, inline)]
Le mar. 20 déc. 2016 à 08:38, Andreas Tille <tille@debian.org> a écrit : > Hi Olivier and Ximin, > > I stripped the quote of the build log below but to me it seems to be > related to the jmol upgrade. > I saw the bug this morning, I gonna have a look > > Any help to get this fixed would be really welcome. > > Kind regards > > Andreas. > > On Mon, Dec 19, 2016 at 10:08:48PM +0100, Lucas Nussbaum wrote: > > Source: biojava4-live > > Version: 4.2.4+dfsg-1 > > Severity: serious > > Tags: stretch sid > > User: debian-qa@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. > > ... > > > [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 > > -- > http://fam-tille.de >
[Message part 2 (text/html, inline)]
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#848768; Package src:biojava4-live.
(Tue, 20 Dec 2016 09:48:03 GMT) (full text, mbox, link).
Acknowledgement sent
to olivier sallou <olivier.sallou@gmail.com>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Tue, 20 Dec 2016 09:48:03 GMT) (full text, mbox, link).
Message #20 received at 848768@bugs.debian.org (full text, mbox, reply):
[Message part 1 (text/plain, inline)]
Le mar. 20 déc. 2016 à 08:55, olivier sallou <olivier.sallou@gmail.com> a écrit : > Le mar. 20 déc. 2016 à 08:38, Andreas Tille <tille@debian.org> a écrit : > > Hi Olivier and Ximin, > > I stripped the quote of the build log below but to me it seems to be > related to the jmol upgrade. > > jmol is still in 12.2.32, looks like to be an other pb, I am investigating > > I saw the bug this morning, I gonna have a look > > > Any help to get this fixed would be really welcome. > > Kind regards > > Andreas. > > On Mon, Dec 19, 2016 at 10:08:48PM +0100, Lucas Nussbaum wrote: > > Source: biojava4-live > > Version: 4.2.4+dfsg-1 > > Severity: serious > > Tags: stretch sid > > User: debian-qa@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. > > ... > > > [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 > > -- > http://fam-tille.de > >
[Message part 2 (text/html, inline)]
Reply sent
to Olivier Sallou <osallou@debian.org>:
You have taken responsibility.
(Tue, 20 Dec 2016 10:51:07 GMT) (full text, mbox, link).
Notification sent
to Lucas Nussbaum <lucas@debian.org>:
Bug acknowledged by developer.
(Tue, 20 Dec 2016 10:51:07 GMT) (full text, mbox, link).
Message #25 received at 848768-close@bugs.debian.org (full text, mbox, reply):
Source: biojava4-live
Source-Version: 4.2.4+dfsg-2
We believe that the bug you reported is fixed in the latest version of
biojava4-live, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 848768@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <osallou@debian.org> (supplier of updated biojava4-live package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 20 Dec 2016 10:48:01 +0100
Source: biojava4-live
Binary: libbiojava4.0-java libbiojava4-java libbiojava4-java-doc
Architecture: source all
Version: 4.2.4+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osallou@debian.org>
Description:
libbiojava4-java - Java API to biological data and applications (default version)
libbiojava4-java-doc - [Biology] Documentation for BioJava
libbiojava4.0-java - Java API to biological data and applications (version 4)
Closes: 848768
Changes:
biojava4-live (4.2.4+dfsg-2) unstable; urgency=medium
.
* d/control: add jgrapht as required dependency instead of suggests
(Closes: #848768)
Checksums-Sha1:
79baf7d83bcf4044f7d87943548d1e68207e4006 2636 biojava4-live_4.2.4+dfsg-2.dsc
bf104d0f4bc2ab101a57988da4ca8654730777f8 14144 biojava4-live_4.2.4+dfsg-2.debian.tar.xz
164b682cebfd14d92fdc942873971e7f550d76a7 10865 biojava4-live_4.2.4+dfsg-2_amd64.buildinfo
e326455a5d0614abdc7affbb6a7d5fa0a55b2735 1660636 libbiojava4-java-doc_4.2.4+dfsg-2_all.deb
c94801a5be157272e3a12aa8b26b814a318ef263 3622 libbiojava4-java_4.2.4+dfsg-2_all.deb
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Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#848768; Package src:biojava4-live.
(Tue, 20 Dec 2016 11:45:02 GMT) (full text, mbox, link).
Acknowledgement sent
to Ximin Luo <infinity0@debian.org>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Tue, 20 Dec 2016 11:45:02 GMT) (full text, mbox, link).
Message #30 received at 848768@bugs.debian.org (full text, mbox, reply):
Hey all, Indeed, jmol in unstable is still version 12. If biojava4-live 4.2.4 is supposed to work with 14, that would be the problem. I will upload jmol 14 to unstable in the next 2-3 hours, you can try it again with that. Perhaps it would already solve this FTBFS. X olivier sallou: > Le mar. 20 déc. 2016 à 08:55, olivier sallou <olivier.sallou@gmail.com> a > écrit : > >> Le mar. 20 déc. 2016 à 08:38, Andreas Tille <tille@debian.org> a écrit : >> >> Hi Olivier and Ximin, >> >> I stripped the quote of the build log below but to me it seems to be >> related to the jmol upgrade. >> >> > jmol is still in 12.2.32, looks like to be an other pb, I am investigating > > >> >> I saw the bug this morning, I gonna have a look >> >> >> Any help to get this fixed would be really welcome. >> >> Kind regards >> >> Andreas. >> >> On Mon, Dec 19, 2016 at 10:08:48PM +0100, Lucas Nussbaum wrote: >>> Source: biojava4-live >>> Version: 4.2.4+dfsg-1 >>> Severity: serious >>> Tags: stretch sid >>> User: debian-qa@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. >>> ... >>>> [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 >> >> -- >> http://fam-tille.de >> >> > -- GPG: ed25519/56034877E1F87C35 GPG: rsa4096/1318EFAC5FBBDBCE https://github.com/infinity0/pubkeys.git
Information forwarded
to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#848768; Package src:biojava4-live.
(Tue, 20 Dec 2016 12:03:03 GMT) (full text, mbox, link).
Acknowledgement sent
to olivier sallou <olivier.sallou@gmail.com>:
Extra info received and forwarded to list. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Tue, 20 Dec 2016 12:03:03 GMT) (full text, mbox, link).
Message #35 received at 848768@bugs.debian.org (full text, mbox, reply):
[Message part 1 (text/plain, inline)]
I have already fixed the issue. The problem was a library previously in suggest for runtime is now needed for build. Le mar. 20 déc. 2016 à 12:43, Ximin Luo <infinity0@debian.org> a écrit : > Hey all, > > Indeed, jmol in unstable is still version 12. If biojava4-live 4.2.4 is > supposed to work with 14, that would be the problem. > > I will upload jmol 14 to unstable in the next 2-3 hours, you can try it > again with that. Perhaps it would already solve this FTBFS. > > X > > olivier sallou: > > Le mar. 20 déc. 2016 à 08:55, olivier sallou <olivier.sallou@gmail.com> > a > > écrit : > > > >> Le mar. 20 déc. 2016 à 08:38, Andreas Tille <tille@debian.org> a écrit > : > >> > >> Hi Olivier and Ximin, > >> > >> I stripped the quote of the build log below but to me it seems to be > >> related to the jmol upgrade. > >> > >> > > jmol is still in 12.2.32, looks like to be an other pb, I am > investigating > > > > > >> > >> I saw the bug this morning, I gonna have a look > >> > >> > >> Any help to get this fixed would be really welcome. > >> > >> Kind regards > >> > >> Andreas. > >> > >> On Mon, Dec 19, 2016 at 10:08:48PM +0100, Lucas Nussbaum wrote: > >>> Source: biojava4-live > >>> Version: 4.2.4+dfsg-1 > >>> Severity: serious > >>> Tags: stretch sid > >>> User: debian-qa@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. > >>> ... > >>>> [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 > >> > >> -- > >> http://fam-tille.de > >> > >> > > > > > -- > GPG: ed25519/56034877E1F87C35 > GPG: rsa4096/1318EFAC5FBBDBCE > https://github.com/infinity0/pubkeys.git >
[Message part 2 (text/html, inline)]
Bug archived.
Request was from Debbugs Internal Request <owner@bugs.debian.org>
to internal_control@bugs.debian.org.
(Sat, 04 Feb 2017 07:34:35 GMT) (full text, mbox, link).
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