Source: biojava3-live
Version: 3.0.7+dfsg-1
Severity: serious
Tags: jessie sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20140510 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»/biojava3-live-3.0.7+dfsg'
> cd biojava3-forester && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-forester/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-forester/classes
> [mkdir] Created dir: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-forester/build.xml:72: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> [javac] Compiling 332 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-forester/classes
> [javac] Note:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
> uses or overrides a deprecated API.
> [javac] Note: Recompile with -Xlint:deprecation for details.
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [copy] Warning:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-forester/src/main/resources
> does not exist.
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-forester.jar
>
> BUILD SUCCESSFUL
> Total time: 13 seconds
> cd biojava3-core && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-core/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-core/classes
> [javac] /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-core/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 134 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-core/classes
> [javac] Note:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-core/src/main/java/org/biojava3/core/sequence/ProteinSequence.java
> uses unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [copy] Copying 1 file to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-core/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-core.jar
>
> BUILD SUCCESSFUL
> Total time: 6 seconds
> cd biojava3-phylo && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-phylo/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-phylo/classes
> [javac] /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-phylo/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 10 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-phylo/classes
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [copy] Copying 1 file to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-phylo/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-phylo.jar
>
> BUILD SUCCESSFUL
> Total time: 3 seconds
> cd biojava3-alignment && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-alignment/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-alignment/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-alignment/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 65 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-alignment/classes
> [copy] Copying 20 files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-alignment/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-alignment.jar
>
> BUILD SUCCESSFUL
> Total time: 5 seconds
> cd biojava3-aa-prop && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-aa-prop/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-aa-prop/build.xml:72: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> [javac] Compiling 31 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/xml/package-info.class
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/profeat/convertor/package-info.class
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/package-info.class
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes/org/biojava3/aaproperties/profeat/package-info.class
> [copy] Copying 10 files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-aa-prop/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-aa-prop.jar
>
> BUILD SUCCESSFUL
> Total time: 3 seconds
> cd biojava3-genome && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-genome/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-genome/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-genome/build.xml:72: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> [javac] Compiling 20 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-genome/classes
> [javac] Note:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-genome/src/main/java/org/biojava3/genome/parsers/gff/GFF3Writer.java
> uses unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [copy] Warning:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-genome/src/main/resources does
> not exist.
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-genome.jar
>
> BUILD SUCCESSFUL
> Total time: 4 seconds
> cd biojava3-sequencing && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-sequencing/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-sequencing/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-sequencing/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 19 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-sequencing/classes
> [javac] Note:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-sequencing/src/main/java/org/biojava3/sequencing/io/fastq/FastqTools.java
> uses unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-sequencing/classes/org/biojava3/sequencing/io/fastq/package-info.class
> [copy] Warning:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-sequencing/src/main/resources
> does not exist.
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-sequencing.jar
>
> BUILD SUCCESSFUL
> Total time: 3 seconds
> cd biojava3-structure && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-structure/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-structure/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-structure/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 314 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-structure/classes
> [javac] Note: Some input files use or override a deprecated API.
> [javac] Note: Recompile with -Xlint:deprecation for details.
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [copy] Copying 63 files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-structure/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-structure.jar
>
> BUILD SUCCESSFUL
> Total time: 11 seconds
> cd biojava3-structure-gui && ant jar
> Buildfile:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-structure-gui/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-structure-gui/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 105 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-structure-gui/classes
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [copy] Copying 14 files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-structure-gui/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-structure-gui.jar
>
> BUILD SUCCESSFUL
> Total time: 8 seconds
> cd biojava3-modfinder && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-modfinder/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-modfinder/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-modfinder/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 21 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-modfinder/classes
> [copy] Copying 1 file to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-modfinder/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-modfinder.jar
>
> BUILD SUCCESSFUL
> Total time: 4 seconds
> cd biojava3-protein-disorder && ant jar
> Buildfile:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-protein-disorder/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-protein-disorder/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 13 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes/org/biojava3/data/sequence/package-info.class
> [javac] Creating empty
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes/org/biojava3/ronn/package-info.class
> [copy] Copying 10 files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-protein-disorder/classes
>
> jar:
> [jar] Building jar:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/dist/biojava3-protein-disorder.jar
>
> BUILD SUCCESSFUL
> Total time: 3 seconds
> cd biojava3-ws && ant jar
> Buildfile: /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/build.xml
>
> compile:
> [mkdir] Created dir:
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-ws/classes
> [javac] /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/build.xml:72:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> [javac] Compiling 20 source files to
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/build/biojava3-ws/classes
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:16:
> error: package org.json.simple does not exist
> [javac] import org.json.simple.JSONArray;
> [javac] ^
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:17:
> error: package org.json.simple does not exist
> [javac] import org.json.simple.JSONObject;
> [javac] ^
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:18:
> error: package org.json.simple does not exist
> [javac] import org.json.simple.JSONValue;
> [javac] ^
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:106:
> error: cannot find symbol
> [javac] JSONObject json= (JSONObject)
> JSONValue.parse(result.toString());
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:106:
> error: cannot find symbol
> [javac] JSONObject json= (JSONObject)
> JSONValue.parse(result.toString());
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:106:
> error: cannot find symbol
> [javac] JSONObject json= (JSONObject)
> JSONValue.parse(result.toString());
> [javac] ^
> [javac] symbol: variable JSONValue
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:107:
> error: cannot find symbol
> [javac] JSONObject hmresults = (JSONObject)
> json.get("results");
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:107:
> error: cannot find symbol
> [javac] JSONObject hmresults = (JSONObject)
> json.get("results");
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:109:
> error: cannot find symbol
> [javac] JSONArray hits = (JSONArray)
> hmresults.get("hits");
> [javac] ^
> [javac] symbol: class JSONArray
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:109:
> error: cannot find symbol
> [javac] JSONArray hits = (JSONArray)
> hmresults.get("hits");
> [javac] ^
> [javac] symbol: class JSONArray
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:112:
> error: cannot find symbol
> [javac] JSONObject hit = (JSONObject)
> hits.get(i);
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:112:
> error: cannot find symbol
> [javac] JSONObject hit = (JSONObject)
> hits.get(i);
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:136:
> error: cannot find symbol
> [javac] JSONArray hmmdomains = (JSONArray)
> hit.get("domains");
> [javac] ^
> [javac] symbol: class JSONArray
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:136:
> error: cannot find symbol
> [javac] JSONArray hmmdomains = (JSONArray)
> hit.get("domains");
> [javac] ^
> [javac] symbol: class JSONArray
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:140:
> error: cannot find symbol
> [javac] JSONObject d = (JSONObject)
> hmmdomains.get(j);
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac]
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/src/main/java/org/biojava3/ws/hmmer/RemoteHmmerScan.java:140:
> error: cannot find symbol
> [javac] JSONObject d = (JSONObject)
> hmmdomains.get(j);
> [javac] ^
> [javac] symbol: class JSONObject
> [javac] location: class RemoteHmmerScan
> [javac] 16 errors
>
> BUILD FAILED
> /«BUILDDIR»/biojava3-live-3.0.7+dfsg/biojava3-ws/build.xml:72: Compile
> failed; see the compiler error output for details.
>
> Total time: 3 seconds
> make[1]: *** [override_dh_auto_build] Error 1
The full build log is available from:
http://aws-logs.debian.net/ftbfs-logs/2014/05/10/biojava3-live_3.0.7+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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