SuccessConsole Output

Started by an SCM change
Building remotely on i-0404a965 in workspace /media/ephemeral0/workspace/phyloutils
[phyloutils] $ hg showconfig paths.default
[phyloutils] $ hg pull --rev default
[phyloutils] $ hg update --clean --rev default
1 files updated, 0 files merged, 0 files removed, 0 files unresolved
[phyloutils] $ hg --config extensions.purge= clean --all
[phyloutils] $ hg log --rev . --template {node}
[phyloutils] $ hg log --rev . --template {rev}
[phyloutils] $ hg log --rev 070e759ffe4f76a761ce5ff1db067c9f3639078c
[phyloutils] $ hg log --template "<changeset node='{node}' author='{author|xmlescape}' rev='{rev}' date='{date}'><msg>{desc|xmlescape}</msg><added>{file_adds|stringify|xmlescape}</added><deleted>{file_dels|stringify|xmlescape}</deleted><files>{files|stringify|xmlescape}</files><parents>{parents}</parents></changeset>\n" --rev default:0 --follow --prune 070e759ffe4f76a761ce5ff1db067c9f3639078c
Parsing POMs
Modules changed, recalculating dependency graph
[phyloutils] $ java -Xmx1024M -XX:MaxPermSize=256M -cp /media/ephemeral0/maven3-agent.jar:/media/ephemeral0/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.4/boot/plexus-classworlds-2.4.jar org.jvnet.hudson.maven3.agent.Maven3Main /media/ephemeral0/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.0.4 /tmp/slave.jar /media/ephemeral0/maven3-interceptor.jar 46962
<===[JENKINS REMOTING CAPACITY]===>channel started
log4j:WARN No appenders could be found for logger (org.apache.commons.beanutils.converters.BooleanConverter).
log4j:WARN Please initialize the log4j system properly.
Executing Maven:  -B -f /media/ephemeral0/workspace/phyloutils/pom.xml -U -e clean source:jar package jar:test-jar
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-metadata.xml
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building phyloutils 0.93-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://dev.davidsoergel.com/nexus/content/groups/public/com/davidsoergel/conja/1.051/conja-1.051.pom
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[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ phyloutils ---
[INFO] 
[INFO] --- cobertura-maven-plugin:2.5.1:clean (clean) @ phyloutils ---
Mar 21, 2013 2:52:24 AM hudson.maven.ExecutedMojo <init>
WARNING: Failed to getClass for org.apache.maven.plugin.source.SourceJarMojo
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar (default-cli) @ phyloutils ---
[INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.93-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ phyloutils ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ phyloutils ---
[INFO] Compiling 35 source files to /media/ephemeral0/workspace/phyloutils/target/classes
[WARNING] /media/ephemeral0/workspace/phyloutils/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[11,45] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[WARNING] /media/ephemeral0/workspace/phyloutils/src/main/java/edu/berkeley/compbio/phyloutils/NewickWithSynonymsAndRanksTaxonomyService.java:[277,12] sun.reflect.generics.reflectiveObjects.NotImplementedException is Sun proprietary API and may be removed in a future release
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ phyloutils ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 4 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ phyloutils ---
[INFO] Compiling 4 source files to /media/ephemeral0/workspace/phyloutils/target/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ phyloutils ---
[INFO] Surefire report directory: /media/ephemeral0/workspace/phyloutils/target/surefire-reports

-------------------------------------------------------
 T E S T S
-------------------------------------------------------
Running TestSuite
2013-03-21 02:53:27,207 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2013-03-21 02:53:27,487 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/edu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2013-03-21 02:53:27,490 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2013-03-21 02:53:27,626 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2013-03-21 02:53:27,688 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2013-03-21 02:53:27,688 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2013-03-21 02:53:27,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2013-03-21 02:53:27,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2013-03-21 02:53:27,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2013-03-21 02:53:27,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2013-03-21 02:53:27,689 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2013-03-21 02:53:27,690 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2013-03-21 02:53:27,699 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2013-03-21 02:53:27,699 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2013-03-21 02:53:27,699 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2013-03-21 02:53:27,700 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2013-03-21 02:53:27,701 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2013-03-21 02:53:27,707 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2013-03-21 02:53:27,707 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2013-03-21 02:53:27,707 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2013-03-21 02:53:27,707 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2013-03-21 02:53:27,707 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2013-03-21 02:53:27,708 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2013-03-21 02:53:27,708 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2013-03-21 02:53:27,708 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2013-03-21 02:53:27,708 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2013-03-21 02:53:27,708 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2013-03-21 02:53:27,708 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2013-03-21 02:53:27,709 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2013-03-21 02:53:27,714 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2013-03-21 02:53:27,714 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2013-03-21 02:53:27,714 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2013-03-21 02:53:27,714 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2013-03-21 02:53:27,715 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2013-03-21 02:53:27,716 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2013-03-21 02:53:27,720 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2013-03-21 02:53:27,720 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2013-03-21 02:53:27,720 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2013-03-21 02:53:27,720 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2013-03-21 02:53:27,721 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2013-03-21 02:53:27,721 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2013-03-21 02:53:27,721 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2013-03-21 02:53:27,721 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2013-03-21 02:53:27,721 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2013-03-21 02:53:27,722 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2013-03-21 02:53:27,722 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2013-03-21 02:53:27,725 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2013-03-21 02:53:27,725 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2013-03-21 02:53:27,725 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2013-03-21 02:53:27,725 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2013-03-21 02:53:27,726 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2013-03-21 02:53:27,726 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 6
BasicRootedPhylogeny{root}
Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.058 sec

Results :

Tests run: 6, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ phyloutils ---
[INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.93-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ phyloutils ---
[INFO] Building jar: /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.93-SNAPSHOT-tests.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default) @ phyloutils ---
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default-cli) @ phyloutils ---
[WARNING] Artifact edu.berkeley.compbio:phyloutils:test-jar:tests:0.93-SNAPSHOT already attached to project, ignoring duplicate
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2:18.634s
[INFO] Finished at: Thu Mar 21 02:53:58 UTC 2013
[INFO] Final Memory: 15M/37M
[INFO] ------------------------------------------------------------------------
[JENKINS] Archiving /media/ephemeral0/workspace/phyloutils/pom.xml to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/modules/edu.berkeley.compbio$phyloutils/builds/2013-03-20_22-51-21/archive/edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT.pom
[JENKINS] Archiving /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.93-SNAPSHOT.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/modules/edu.berkeley.compbio$phyloutils/builds/2013-03-20_22-51-21/archive/edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT.jar
[JENKINS] Archiving /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.93-SNAPSHOT-sources.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/modules/edu.berkeley.compbio$phyloutils/builds/2013-03-20_22-51-21/archive/edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT-sources.jar
[JENKINS] Archiving /media/ephemeral0/workspace/phyloutils/target/phyloutils-0.93-SNAPSHOT-tests.jar to /usr/share/apache-tomcat-7.0.22/.jenkins/jobs/phyloutils/modules/edu.berkeley.compbio$phyloutils/builds/2013-03-20_22-51-21/archive/edu.berkeley.compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-SNAPSHOT-tests.jar
Waiting for Jenkins to finish collecting data
channel stopped
Maven RedeployPublisher use remote i-0404a965 maven settings from : /home/ec2-user/.m2/settings.xml
[ERROR] uniqueVersion == false is not anymore supported in maven 3
[INFO] Deployment in dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots (id=dev.davidsoergel.com.snapshot,uniqueVersion=false)
Deploying the main artifact phyloutils-0.93-SNAPSHOT.jar
Downloading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
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Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2.jar
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2.jar (2793 KB at 4453.1 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2.pom
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2.pom (7 KB at 29.7 KB/sec)
Downloading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml
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Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml (2 KB at 5.0 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/maven-metadata.xml (348 B at 2.5 KB/sec)
Deploying the main artifact phyloutils-0.93-SNAPSHOT-sources.jar
Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2-sources.jar
Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2-sources.jar (2779 KB at 4600.0 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
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Deploying the main artifact phyloutils-0.93-SNAPSHOT-tests.jar
Uploading: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2-tests.jar
Uploaded: dav:http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/phyloutils-0.93-20130321.025431-2-tests.jar (11 KB at 63.5 KB/sec)
Uploading: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml
Uploaded: http://dev.davidsoergel.com/nexus/content/repositories/snapshots/edu/berkeley/compbio/phyloutils/0.93-SNAPSHOT/maven-metadata.xml (2 KB at 17.8 KB/sec)
[INFO] Deployment done in 2.8 sec
Sending e-mails to: dev@davidsoergel.com
Triggering a new build of msensr #19
Finished: SUCCESS