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Progress (2): 1.1/3.2 MB | 344/424 kB Progress (2): 1.1/3.2 MB | 360/424 kB Progress (2): 1.1/3.2 MB | 377/424 kB Progress (2): 1.1/3.2 MB | 393/424 kB Progress (2): 1.1/3.2 MB | 410/424 kB Progress (2): 1.1/3.2 MB | 424 kB Downloaded from central: https://repo.maven.apache.org/maven2/biz/aQute/bnd/biz.aQute.bnd.util/6.3.1/biz.aQute.bnd.util-6.3.1.jar (424 kB at 2.4 MB/s) Progress (2): 1.1/3.2 MB | 16/614 kB Progress (2): 1.1/3.2 MB | 33/614 kB Progress (2): 1.1/3.2 MB | 49/614 kB Progress (3): 1.1/3.2 MB | 49/614 kB | 16/52 kB Progress (4): 1.1/3.2 MB | 49/614 kB | 16/52 kB | 16/26 kB Progress (4): 1.1/3.2 MB | 49/614 kB | 16/52 kB | 26 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/3.5.2/maven-archiver-3.5.2.jar (26 kB at 143 kB/s) Progress (3): 1.1/3.2 MB | 66/614 kB | 16/52 kB Progress (3): 1.1/3.2 MB | 82/614 kB | 16/52 kB Progress (3): 1.1/3.2 MB | 98/614 kB | 16/52 kB Progress (3): 1.1/3.2 MB | 115/614 kB | 16/52 kB Progress (3): 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kB/s) Progress (2): 2.7/3.2 MB | 0.2/1.5 MB Progress (2): 2.7/3.2 MB | 0.2/1.5 MB Progress (2): 2.7/3.2 MB | 0.2/1.5 MB Progress (2): 2.7/3.2 MB | 0.2/1.5 MB Progress (2): 2.7/3.2 MB | 0.2/1.5 MB Progress (2): 2.7/3.2 MB | 0.2/1.5 MB Progress (2): 2.7/3.2 MB | 0.3/1.5 MB Progress (2): 2.7/3.2 MB | 0.3/1.5 MB Progress (2): 2.7/3.2 MB | 0.3/1.5 MB Progress (2): 2.7/3.2 MB | 0.3/1.5 MB Progress (2): 2.7/3.2 MB | 0.3/1.5 MB Progress (3): 2.7/3.2 MB | 0.3/1.5 MB | 16/50 kB Progress (3): 2.7/3.2 MB | 0.3/1.5 MB | 33/50 kB Progress (3): 2.7/3.2 MB | 0.3/1.5 MB | 49/50 kB Progress (3): 2.7/3.2 MB | 0.3/1.5 MB | 50 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-classworlds/2.5.1/plexus-classworlds-2.5.1.jar (50 kB at 129 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/plexus/plexus-sec-dispatcher/1.3/plexus-sec-dispatcher-1.3.jar Progress (2): 2.7/3.2 MB | 0.3/1.5 MB Progress (2): 2.7/3.2 MB | 0.4/1.5 MB Progress 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(2): 420/571 kB | 147/153 kB Progress (2): 420/571 kB | 153 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/jdom/jdom/1.1/jdom-1.1.jar (153 kB at 247 kB/s) Progress (1): 436/571 kB Progress (1): 452/571 kB Progress (1): 469/571 kB Progress (1): 485/571 kB Progress (1): 502/571 kB Progress (1): 518/571 kB Progress (1): 534/571 kB Progress (1): 551/571 kB Progress (1): 567/571 kB Progress (1): 571 kB Downloaded from central: https://repo.maven.apache.org/maven2/commons-collections/commons-collections/3.2/commons-collections-3.2.jar (571 kB at 904 kB/s) Progress (1): 16/22 kB Progress (1): 22 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-module-xhtml/1.0/doxia-module-xhtml-1.0.jar (22 kB at 34 kB/s) [WARNING] [WARNING] Some problems were encountered while building the effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.slf4j:slf4j-api:jar -> duplicate declaration of version (?) @ line 58, column 21 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] IGB Project [pom] [INFO] Flatlaf - Look and feel configuration [bundle] [INFO] Core - Heatmap Editor [bundle] [INFO] Core - Affymetrix Common [bundle] [INFO] Plugin - Sorting API and Impl [bundle] [INFO] Plugin - Data caching API [bundle] [INFO] Core - Synonym Lookup [bundle] [INFO] Core - Genometry (Data Models) [bundle] [INFO] Core - Preferences [bundle] [INFO] Core - IGB Swing Extensions [bundle] [INFO] Core - Genoviz Extensions [bundle] [INFO] Core - IGB Services API [bundle] [INFO] Core - Frame Manager [bundle] [INFO] Core - Window Service [bundle] [INFO] Core - JavaFX Utilities [bundle] [INFO] Core - Menu API [bundle] [INFO] Core - Context Menu Service [bundle] [INFO] Core - IGB [bundle] [INFO] Core - Bundle wrapper, deployer [bundle] [INFO] Core - Logging Config [bundle] [INFO] Core - Web Links [bundle] [INFO] Plugin - Data caching GUI [bundle] [INFO] Core - Quickload (data source) [bundle] [INFO] Core - DAS (data source) [bundle] [INFO] Plugin - Apollo Library [bundle] [INFO] Plugin - Track Operations API, GUI [bundle] [INFO] Plugin - Annotation Tab [bundle] [INFO] Plugin - Console Tab [bundle] [INFO] Plugin - Bigbed data format handler [bundle] [INFO] Plugin - Bigwig data format handler [bundle] [INFO] Plugin - Bookmarks and REST API [bundle] [INFO] Plugin - External View [bundle] [INFO] Plugin - Graph Tab [bundle] [INFO] Plugin - Save Image GUI [bundle] [INFO] Plugin - Script handler [bundle] [INFO] Plugin - Keyword Search [bundle] [INFO] Plugin - NCBI Blast [bundle] [INFO] Plugin - Selection Info tab [bundle] [INFO] Plugin - Restriction Sites tab [bundle] [INFO] Plugin - Search Id or Props [bundle] [INFO] Plugin - Advanced Search Tab [bundle] [INFO] Plugin - Sequence Viewer GUI [bundle] [INFO] Plugin - Survey GUI [bundle] [INFO] Plugin - Graph thresholding visual analytics [bundle] [INFO] Plugin - Update [bundle] [INFO] Plugin - App Manager GUI [bundle] [INFO] Plugin - Paired-end Read Preprocessor [bundle] [INFO] Plugin - Save Session Manager [bundle] [INFO] Plugin - Toolbar Preferences GUI [bundle] [INFO] Plugin - Feedback [bundle] [INFO] Plugin - Narrowpeak data format handler [bundle] [INFO] Plugin - File Handler - Genotyping Results [bundle] [INFO] Plugin - BED file format handler [bundle] [INFO] Plugin - BAM data format handler [bundle] [INFO] Plugin - BAI index visualization handler [bundle] [INFO] Plugin - App Store REST API [bundle] [INFO] IGB Main (run me) [jar] [INFO] [INFO] -------------------< org.lorainelab.igb:igb-project >------------------- [INFO] Building IGB Project 10.0.0 [1/57] [INFO] from pom.xml [INFO] --------------------------------[ pom ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-install-plugin/3.1.1/maven-install-plugin-3.1.1.pom Progress (1): 7.8 kB Downloaded from central: 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[2/57] [INFO] from plugins/flatlaf/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/maven-metadata.xml Progress (1): 936 B Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/maven-metadata.xml (936 B at 234 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.3.1/maven-resources-plugin-3.3.1.pom Progress (1): 8.2 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.3.1/maven-resources-plugin-3.3.1.pom (8.2 kB at 429 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-resources-plugin/3.3.1/maven-resources-plugin-3.3.1.jar Progress (1): 16/31 kB Progress (1): 31 kB Downloaded from central: 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org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.util.concurrency.RunnableErrorForwarder.lambda$wrap$0 (RunnableErrorForwarder.java:66) at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1144) at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:642) at java.lang.Thread.run (Thread.java:1583) [WARNING] Checksum validation failed, no checksums available from repo2 for https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.jar Downloaded from repo2: https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.jar (8.1 MB at 12 MB/s) Downloading from repo3: 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maven-releases: https://nexus.bioviz.org/repository/maven-releases/ch/qos/logback/logback-core/1.2.12/logback-core-1.2.12.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/ch/qos/logback/logback-classic/1.2.12/logback-classic-1.2.12.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/osgi/org.osgi.service.component.annotations/1.5.1/org.osgi.service.component.annotations-1.5.1.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/osgi/osgi.annotation/8.1.0/osgi.annotation-8.1.0.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/osgi/org.osgi.namespace.extender/1.0.1/org.osgi.namespace.extender-1.0.1.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/osgi/org.osgi.util.promise/1.3.0/org.osgi.util.promise-1.3.0.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/formdev/flatlaf/3.2.5/flatlaf-3.2.5.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/formdev/flatlaf-jide-oss/3.2.5/flatlaf-jide-oss-3.2.5.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.main/7.0.5/org.apache.felix.main-7.0.5.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.framework/7.0.5/org.apache.felix.framework-7.0.5.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/codehaus/mojo/animal-sniffer-annotations/1.9/animal-sniffer-annotations-1.9.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/ch/qos/logback/logback-core/1.2.12/logback-core-1.2.12.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/ch/qos/logback/logback-classic/1.2.12/logback-classic-1.2.12.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/osgi/org.osgi.service.component.annotations/1.5.1/org.osgi.service.component.annotations-1.5.1.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/osgi/osgi.annotation/8.1.0/osgi.annotation-8.1.0.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/osgi/org.osgi.namespace.extender/1.0.1/org.osgi.namespace.extender-1.0.1.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/osgi/org.osgi.util.promise/1.3.0/org.osgi.util.promise-1.3.0.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/formdev/flatlaf/3.2.5/flatlaf-3.2.5.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/formdev/flatlaf-jide-oss/3.2.5/flatlaf-jide-oss-3.2.5.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.main/7.0.5/org.apache.felix.main-7.0.5.jar Progress (1): 16/782 kB Progress (1): 32/782 kB Progress (1): 49/782 kB Progress (1): 65/782 kB Progress (1): 81/782 kB Progress (1): 98/782 kB Progress (1): 114/782 kB Progress (1): 131/782 kB Progress (1): 147/782 kB Progress (1): 163/782 kB Progress (1): 180/782 kB Progress (1): 196/782 kB Progress (1): 212/782 kB Progress (1): 229/782 kB Progress (1): 245/782 kB Progress (1): 262/782 kB Progress (1): 278/782 kB Progress (1): 294/782 kB Progress (1): 311/782 kB Progress (1): 327/782 kB Progress (1): 344/782 kB Progress (1): 360/782 kB Progress (1): 376/782 kB Progress (1): 393/782 kB Progress (1): 409/782 kB Progress (1): 425/782 kB Progress (1): 442/782 kB Progress (1): 458/782 kB Progress (1): 475/782 kB Progress (1): 491/782 kB Progress (1): 507/782 kB Progress (1): 524/782 kB Progress (1): 540/782 kB Progress (1): 557/782 kB Progress (1): 573/782 kB Progress (1): 589/782 kB Progress (1): 606/782 kB Progress (1): 622/782 kB Progress (1): 638/782 kB Progress (1): 655/782 kB Progress (1): 671/782 kB Progress (1): 688/782 kB Progress (1): 704/782 kB Progress (1): 720/782 kB Progress (1): 737/782 kB Progress (1): 753/782 kB Progress (1): 770/782 kB Progress (1): 782 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.main/7.0.5/org.apache.felix.main-7.0.5.jar (782 kB at 23 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.framework/7.0.5/org.apache.felix.framework-7.0.5.jar Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/animal-sniffer-annotations/1.9/animal-sniffer-annotations-1.9.jar Downloading from central: 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| 164/449 kB Progress (2): 360/778 kB | 180/449 kB Progress (2): 360/778 kB | 197/449 kB Progress (2): 360/778 kB | 213/449 kB Progress (2): 360/778 kB | 229/449 kB Downloading from central: https://repo.maven.apache.org/maven2/ch/qos/logback/logback-classic/1.2.12/logback-classic-1.2.12.jar Downloading from central: https://repo.maven.apache.org/maven2/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar Progress (3): 360/778 kB | 229/449 kB | 3.4 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/animal-sniffer-annotations/1.9/animal-sniffer-annotations-1.9.jar (3.4 kB at 126 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/osgi/org.osgi.service.component.annotations/1.5.1/org.osgi.service.component.annotations-1.5.1.jar Progress (3): 360/778 kB | 229/449 kB | 16/43 kB Progress (3): 360/778 kB | 229/449 kB | 33/43 kB Progress (3): 360/778 kB | 229/449 kB | 43 kB Downloaded from central: 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[INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ flatlaf --- [WARNING] Bundle org.lorainelab.igb:flatlaf:bundle:10.0.0 : Classes found in the wrong directory: {META-INF/versions/9/com/formdev/flatlaf/util/MultiResolutionImageSupport$MappedMultiResolutionImage.class=com.formdev.flatlaf.util.MultiResolutionImageSupport$MappedMultiResolutionImage, META-INF/versions/9/com/formdev/flatlaf/util/LoggingFacadeImpl.class=com.formdev.flatlaf.util.LoggingFacadeImpl, META-INF/versions/9/com/formdev/flatlaf/ui/StackUtilsImpl.class=com.formdev.flatlaf.ui.StackUtilsImpl, META-INF/versions/9/com/formdev/flatlaf/util/MultiResolutionImageSupport$ProducerMultiResolutionImage.class=com.formdev.flatlaf.util.MultiResolutionImageSupport$ProducerMultiResolutionImage, META-INF/versions/9/com/formdev/flatlaf/util/MultiResolutionImageSupport.class=com.formdev.flatlaf.util.MultiResolutionImageSupport} [INFO] Building bundle: /build/plugins/flatlaf/target/flatlaf-10.0.0.jar [INFO] Writing manifest: 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272/347 kB | 262/457 kB Progress (3): 450 kB | 289/347 kB | 262/457 kB Downloading from central: https://repo.maven.apache.org/maven2/commons-collections/commons-collections/3.2.2/commons-collections-3.2.2.jar Progress (4): 450 kB | 289/347 kB | 262/457 kB | 16/90 kB Progress (4): 450 kB | 289/347 kB | 262/457 kB | 33/90 kB Progress (4): 450 kB | 289/347 kB | 262/457 kB | 49/90 kB Progress (4): 450 kB | 289/347 kB | 262/457 kB | 66/90 kB Progress (4): 450 kB | 289/347 kB | 262/457 kB | 82/90 kB Progress (4): 450 kB | 289/347 kB | 262/457 kB | 90 kB Downloaded from central: https://repo.maven.apache.org/maven2/commons-chain/commons-chain/1.1/commons-chain-1.1.jar (90 kB at 443 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/4.6.0/plexus-archiver-4.6.0.jar Progress (3): 450 kB | 305/347 kB | 262/457 kB Progress (3): 450 kB | 321/347 kB | 262/457 kB Progress (3): 450 kB | 338/347 kB | 262/457 kB Downloaded from central: 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(default-compile) @ heatmap-editor --- [INFO] Changes detected - recompiling the module! :source [INFO] Compiling 14 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ heatmap-editor --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ heatmap-editor --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ heatmap-editor --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ heatmap-editor --- [INFO] Building bundle: /build/core/heatmap-editor/target/heatmap-editor-10.0.0.jar [INFO] Writing manifest: /build/core/heatmap-editor/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ heatmap-editor --- [INFO] Installing /build/core/heatmap-editor/pom.xml to /root/.m2/repository/org/lorainelab/igb/heatmap-editor/10.0.0/heatmap-editor-10.0.0.pom [INFO] Installing /build/core/heatmap-editor/target/heatmap-editor-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/heatmap-editor/10.0.0/heatmap-editor-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ heatmap-editor --- [INFO] Installing org/lorainelab/igb/heatmap-editor/10.0.0/heatmap-editor-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ heatmap-editor --- [INFO] Configured Artifact: org.lorainelab.igb:heatmap-editor:10.0.0:jar [INFO] Copying heatmap-editor-10.0.0.jar to /build/bundles/heatmap-editor-10.0.0.jar [INFO] [INFO] ----------------< org.lorainelab.igb:affymetrix-common >---------------- [INFO] Building Core - Affymetrix Common 10.0.0 [4/57] [INFO] from core/common/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom Downloading from central: https://repo.maven.apache.org/maven2/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom Progress (1): 1.4 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.pom (1.4 kB at 346 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.pom Progress (1): 149 B [WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.pom org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63) at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.connector.basic.BasicRepositoryConnector.get (BasicRepositoryConnector.java:260) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads (DefaultArtifactResolver.java:537) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve (DefaultArtifactResolver.java:449) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts (DefaultArtifactResolver.java:261) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact (DefaultArtifactResolver.java:243) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom (DefaultArtifactDescriptorReader.java:234) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor (DefaultArtifactDescriptorReader.java:175) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.resolveCachedArtifactDescriptor (DfDependencyCollector.java:382) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.getArtifactDescriptorResult (DfDependencyCollector.java:368) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:218) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:156) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.process (DfDependencyCollector.java:138) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.doCollectDependencies (DfDependencyCollector.java:108) at org.eclipse.aether.internal.impl.collect.DependencyCollectorDelegate.collectDependencies (DependencyCollectorDelegate.java:222) at org.eclipse.aether.internal.impl.collect.DefaultDependencyCollector.collectDependencies (DefaultDependencyCollector.java:87) at org.eclipse.aether.internal.impl.DefaultRepositorySystem.collectDependencies (DefaultRepositorySystem.java:306) at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:151) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:224) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:136) at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:355) at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:313) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:212) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:174) at org.apache.maven.lifecycle.internal.MojoExecutor.access$000 (MojoExecutor.java:75) at org.apache.maven.lifecycle.internal.MojoExecutor$1.run (MojoExecutor.java:162) at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute (DefaultMojosExecutionStrategy.java:39) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:159) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:105) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:73) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:53) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:118) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:261) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:173) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:101) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:906) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:283) at org.apache.maven.cli.MavenCli.main (MavenCli.java:206) at jdk.internal.reflect.DirectMethodHandleAccessor.invoke (DirectMethodHandleAccessor.java:103) at java.lang.reflect.Method.invoke (Method.java:580) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:283) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:226) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:407) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:348) [WARNING] Checksum validation failed, no checksums available from repo1 for https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.pom Downloaded from repo1: https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.pom (149 B at 2.5 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.pom Progress (1): 7.6/11 kB Progress (1): 11 kB Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.pom (11 kB at 542 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/affymetrix/genovizProject/1.1.9/genovizProject-1.1.9.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/affymetrix/genovizProject/1.1.9/genovizProject-1.1.9.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/affymetrix/genovizProject/1.1.9/genovizProject-1.1.9.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/affymetrix/genovizProject/1.1.9/genovizProject-1.1.9.pom Progress (1): 3.0 kB Downloaded from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/affymetrix/genovizProject/1.1.9/genovizProject-1.1.9.pom (3.0 kB at 145 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.jar Downloading from repo1: https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar Downloading from repo1: https://maven.bioviz.org/repo1/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.jar Progress (1): 16/115 kB Progress (1): 33/115 kB Progress (1): 49/115 kB Progress (1): 66/115 kB Progress (1): 82/115 kB Progress (1): 98/115 kB Progress (1): 115 kB [WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63) at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.util.concurrency.RunnableErrorForwarder.lambda$wrap$0 (RunnableErrorForwarder.java:66) at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1144) at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:642) at java.lang.Thread.run (Thread.java:1583) [WARNING] Checksum validation failed, no checksums available from repo1 for https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar Downloaded from repo1: https://maven.bioviz.org/repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar (115 kB at 1.7 MB/s) Downloading from repo2: https://maven.bioviz.org/repo2/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.jar Downloading from repo2: https://maven.bioviz.org/repo2/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.jar Downloading from repo3: https://maven.bioviz.org/repo3/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/affymetrix/genoviz/1.1.9/genoviz-1.1.9.jar Progress (1): 0/1.0 MB Progress (1): 0/1.0 MB Progress (1): 0/1.0 MB Progress (1): 0/1.0 MB Progress (1): 0/1.0 MB Progress (1): 0/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.1/1.0 MB Progress (1): 0.2/1.0 MB Progress (1): 0.2/1.0 MB Progress (1): 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https://nexus.bioviz.org/repository/igb-dev/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.jar Downloading from central: https://repo.maven.apache.org/maven2/org/freedesktop/tango/tango-icon-theme/0.8.90/tango-icon-theme-0.8.90.jar Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0.1/1.9 MB Progress (1): 0.1/1.9 MB Progress (1): 0.1/1.9 MB Progress (1): 0.1/1.9 MB Progress (1): 0.1/1.9 MB Progress (1): 0.1/1.9 MB Progress (1): 0.2/1.9 MB Progress (1): 0.2/1.9 MB Progress (1): 0.2/1.9 MB Progress (1): 0.2/1.9 MB Progress (1): 0.2/1.9 MB Progress (1): 0.2/1.9 MB Progress (1): 0.3/1.9 MB Progress (1): 0.3/1.9 MB Progress (1): 0.3/1.9 MB Progress (1): 0.3/1.9 MB Progress (1): 0.3/1.9 MB Progress (1): 0.3/1.9 MB Progress (1): 0.4/1.9 MB Progress (1): 0.4/1.9 MB Progress (1): 0.4/1.9 MB Progress (1): 0.4/1.9 MB Progress (1): 0.4/1.9 MB Progress (1): 0.4/1.9 MB Progress (1): 0.5/1.9 MB Progress (1): 0.5/1.9 MB Progress (1): 0.5/1.9 MB 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[INFO] /build/core/common/src/main/java/com/affymetrix/common/PreferenceUtils.java: /build/core/common/src/main/java/com/affymetrix/common/PreferenceUtils.java uses unchecked or unsafe operations. [INFO] /build/core/common/src/main/java/com/affymetrix/common/PreferenceUtils.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ affymetrix-common --- [INFO] skip non existing resourceDirectory /build/core/common/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ affymetrix-common --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ affymetrix-common --- [INFO] No tests to run. 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https://nexus.bioviz.org/repository/igb-dev/org/junit/platform/junit-platform-launcher/1.8.2/junit-platform-launcher-1.8.2.jar Downloading from central: https://repo.maven.apache.org/maven2/org/junit/platform/junit-platform-launcher/1.8.2/junit-platform-launcher-1.8.2.jar Progress (1): 16/159 kB Progress (1): 33/159 kB Progress (1): 49/159 kB Progress (1): 66/159 kB Progress (1): 82/159 kB Progress (1): 98/159 kB Progress (1): 115/159 kB Progress (1): 131/159 kB Progress (1): 147/159 kB Progress (1): 159 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/junit/platform/junit-platform-launcher/1.8.2/junit-platform-launcher-1.8.2.jar (159 kB at 23 MB/s) [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.externalsort.ExternalSortTest 15:56:24.748 [main] DEBUG com.google.code.externalsorting.ExternalMergeSort - Temp file count: 1 15:56:24.767 [main] INFO org.lorainelab.igb.externalsort.ExternalSortTest - 29.58 ms [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.473 s -- in org.lorainelab.igb.externalsort.ExternalSortTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ external-sort --- [WARNING] Bundle org.lorainelab.igb:external-sort:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/external-sort/target/external-sort-10.0.0.jar [INFO] Writing manifest: /build/plugins/external-sort/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ external-sort --- [INFO] Installing /build/plugins/external-sort/pom.xml to /root/.m2/repository/org/lorainelab/igb/external-sort/10.0.0/external-sort-10.0.0.pom [INFO] Installing /build/plugins/external-sort/target/external-sort-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/external-sort/10.0.0/external-sort-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ external-sort --- [INFO] Installing org/lorainelab/igb/external-sort/10.0.0/external-sort-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ external-sort --- [INFO] Configured Artifact: org.lorainelab.igb:external-sort:10.0.0:jar [INFO] Copying external-sort-10.0.0.jar to /build/bundles/dynamic/external-sort-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:cache-api >-------------------- [INFO] Building Plugin - Data caching API 10.0.0 [6/57] [INFO] from plugins/cache-api/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ cache-api --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/cache-api/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ cache-api --- [INFO] Changes detected - recompiling the module! :source [INFO] Compiling 3 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ cache-api --- [INFO] skip non existing resourceDirectory /build/plugins/cache-api/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ cache-api --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ cache-api --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ cache-api --- [WARNING] Bundle org.lorainelab.igb:cache-api:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/cache-api/target/cache-api-10.0.0.jar [INFO] Writing manifest: /build/plugins/cache-api/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ cache-api --- [INFO] Installing /build/plugins/cache-api/pom.xml to /root/.m2/repository/org/lorainelab/igb/cache-api/10.0.0/cache-api-10.0.0.pom [INFO] Installing /build/plugins/cache-api/target/cache-api-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/cache-api/10.0.0/cache-api-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ cache-api --- [INFO] Installing org/lorainelab/igb/cache-api/10.0.0/cache-api-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ cache-api --- [INFO] Configured Artifact: org.lorainelab.igb:cache-api:10.0.0:jar [INFO] Copying cache-api-10.0.0.jar to /build/bundles/cache-api-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:synonym-lookup >------------------ [INFO] Building Core - Synonym Lookup 10.0.0 [7/57] [INFO] from core/synonym-lookup/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom Progress (1): 16/20 kB Progress (1): 20 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.pom (20 kB at 3.4 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar Progress (1): 16/55 kB Progress (1): 33/55 kB Progress (1): 49/55 kB Progress (1): 55 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-csv/1.10.0/commons-csv-1.10.0.jar (55 kB at 11 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ synonym-lookup --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ synonym-lookup --- [INFO] Changes detected - recompiling the module! :source [INFO] Compiling 9 source files with javac [debug target 21] to target/classes [INFO] /build/core/synonym-lookup/src/main/java/org/lorainelab/igb/synonymlookup/services/impl/SynonymLookup.java: /build/core/synonym-lookup/src/main/java/org/lorainelab/igb/synonymlookup/services/impl/SynonymLookup.java uses or overrides a deprecated API. [INFO] /build/core/synonym-lookup/src/main/java/org/lorainelab/igb/synonymlookup/services/impl/SynonymLookup.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ synonym-lookup --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ synonym-lookup --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ synonym-lookup --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.lorainelab.synonymlookup.test.SynonymLookupTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.462 s -- in com.lorainelab.synonymlookup.test.SynonymLookupTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ synonym-lookup --- [WARNING] Bundle org.lorainelab.igb:synonym-lookup:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/synonym-lookup/target/synonym-lookup-10.0.0.jar [INFO] Writing manifest: /build/core/synonym-lookup/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ synonym-lookup --- [INFO] Installing /build/core/synonym-lookup/pom.xml to /root/.m2/repository/org/lorainelab/igb/synonym-lookup/10.0.0/synonym-lookup-10.0.0.pom [INFO] Installing /build/core/synonym-lookup/target/synonym-lookup-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/synonym-lookup/10.0.0/synonym-lookup-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ synonym-lookup --- [INFO] Installing org/lorainelab/igb/synonym-lookup/10.0.0/synonym-lookup-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ synonym-lookup --- [INFO] Configured Artifact: org.lorainelab.igb:synonym-lookup:10.0.0:jar [INFO] Copying synonym-lookup-10.0.0.jar to /build/bundles/synonym-lookup-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:genometry >-------------------- [INFO] Building Core - Genometry (Data Models) 10.0.0 [8/57] [INFO] from core/genometry/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/org/jdom/jdom/2.0.2/jdom-2.0.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/jdom/jdom/2.0.2/jdom-2.0.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/jdom/jdom/2.0.2/jdom-2.0.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/jdom/jdom/2.0.2/jdom-2.0.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/jdom/jdom/2.0.2/jdom-2.0.2.pom Downloading from central: https://repo.maven.apache.org/maven2/org/jdom/jdom/2.0.2/jdom-2.0.2.pom Progress (1): 4.6 kB Downloaded from 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(3): 566/918 kB | 16/21 kB | 141 kB Progress (3): 582/918 kB | 16/21 kB | 141 kB Progress (3): 599/918 kB | 16/21 kB | 141 kB Progress (3): 615/918 kB | 16/21 kB | 141 kB Progress (3): 631/918 kB | 16/21 kB | 141 kB Progress (3): 648/918 kB | 16/21 kB | 141 kB Progress (3): 664/918 kB | 16/21 kB | 141 kB Progress (3): 681/918 kB | 16/21 kB | 141 kB Progress (3): 697/918 kB | 16/21 kB | 141 kB Progress (3): 713/918 kB | 16/21 kB | 141 kB Progress (3): 713/918 kB | 21 kB | 141 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/angus/angus-activation/1.0.0/angus-activation-1.0.0.jar (21 kB at 269 kB/s) Downloaded from central: https://repo.maven.apache.org/maven2/org/glassfish/jaxb/jaxb-core/4.0.1/jaxb-core-4.0.1.jar (141 kB at 1.8 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/glassfish/jaxb/txw2/4.0.4/txw2-4.0.4.jar Downloading from central: https://repo.maven.apache.org/maven2/com/sun/istack/istack-commons-runtime/4.2.0/istack-commons-runtime-4.2.0.jar Progress (2): 713/918 kB | 16/26 kB Progress (2): 713/918 kB | 26 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/sun/istack/istack-commons-runtime/4.2.0/istack-commons-runtime-4.2.0.jar (26 kB at 303 kB/s) Progress (2): 713/918 kB | 16/73 kB Progress (2): 713/918 kB | 32/73 kB Progress (2): 713/918 kB | 49/73 kB Progress (2): 713/918 kB | 65/73 kB Progress (2): 713/918 kB | 73 kB Downloading from central: https://repo.maven.apache.org/maven2/com/sun/xml/fastinfoset/FastInfoset/2.1.1/FastInfoset-2.1.1.jar Downloaded from central: https://repo.maven.apache.org/maven2/org/glassfish/jaxb/txw2/4.0.4/txw2-4.0.4.jar (73 kB at 833 kB/s) Progress (2): 713/918 kB | 16/318 kB Progress (2): 713/918 kB | 32/318 kB Progress (2): 713/918 kB | 49/318 kB Progress (2): 713/918 kB | 65/318 kB Progress (2): 713/918 kB | 81/318 kB Progress (2): 713/918 kB | 98/318 kB 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Downloaded from central: https://repo.maven.apache.org/maven2/org/glassfish/jaxb/jaxb-runtime/4.0.1/jaxb-runtime-4.0.1.jar (918 kB at 8.7 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ genometry --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ genometry --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 366 source files with javac [debug target 21] to target/classes [INFO] /build/core/genometry/src/main/java/com/affymetrix/genometry/symmetry/impl/SimpleSymWithProps.java: Some input files use or override a deprecated API. [INFO] /build/core/genometry/src/main/java/com/affymetrix/genometry/symmetry/impl/SimpleSymWithProps.java: Recompile with -Xlint:deprecation for details. [INFO] /build/core/genometry/src/main/java/com/affymetrix/genometry/thread/CThreadWorker.java: /build/core/genometry/src/main/java/com/affymetrix/genometry/thread/CThreadWorker.java uses unchecked or unsafe operations. [INFO] /build/core/genometry/src/main/java/com/affymetrix/genometry/thread/CThreadWorker.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ genometry --- [INFO] Copying 58 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ genometry --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 27 source files with javac [debug target 21] to target/test-classes [WARNING] /build/core/genometry/src/test/java/com/affymetrix/genometry/parsers/GFFParserTest.java:[57,26] Float(double) in java.lang.Float has been deprecated and marked for removal [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ genometry --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.affymetrix.genometry.parsers.FastaParserTest using buffer directly: false using fixed length buffer: false done constructing residues via array id: chrQ [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.290 s -- in com.affymetrix.genometry.parsers.FastaParserTest [INFO] Running com.affymetrix.genometry.parsers.TwoBitParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.920 s -- in com.affymetrix.genometry.parsers.TwoBitParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.CntParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s -- in com.affymetrix.genometry.parsers.graph.CntParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.GrParserTest loaded graph data, total points = 10 loaded graph data, total points = 10 loaded graph data, total points = 10 loaded graph data, total points = 2 loaded graph data, total points = 2 [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.174 s -- in com.affymetrix.genometry.parsers.graph.GrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.WiggleParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 s -- in com.affymetrix.genometry.parsers.graph.WiggleParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.ScoredIntervalParserTest number of scores per line: 2 data lines in .sin file: 4 [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.072 s -- in com.affymetrix.genometry.parsers.graph.ScoredIntervalParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.SgrParserTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.256 s -- in com.affymetrix.genometry.parsers.graph.SgrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.BgrParserTest 16, null, null [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 s -- in com.affymetrix.genometry.parsers.graph.BgrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.BarParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 s -- in com.affymetrix.genometry.parsers.graph.BarParserTest [INFO] Running com.affymetrix.genometry.parsers.PSLParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 s -- in com.affymetrix.genometry.parsers.PSLParserTest [INFO] Running com.affymetrix.genometry.parsers.GFFParserTest lines: 33 syms:33 groups:22 results:22 [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s -- in com.affymetrix.genometry.parsers.GFFParserTest [INFO] Running com.affymetrix.genometry.parsers.Bprobe1ParserTest in Bprobe1Parser, populating id hash: true finished parsing probeset file [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s -- in com.affymetrix.genometry.parsers.Bprobe1ParserTest [INFO] Running com.affymetrix.genometry.parsers.TrackLineParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s -- in com.affymetrix.genometry.parsers.TrackLineParserTest [INFO] Running com.affymetrix.genometry.parsers.CytobandParserTest in CytobandParser.writeAnnotations() [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 s -- in com.affymetrix.genometry.parsers.CytobandParserTest [INFO] Running com.affymetrix.genometry.parsers.SamRecordFlagTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 s -- in com.affymetrix.genometry.parsers.SamRecordFlagTest [INFO] Running com.affymetrix.genometry.parsers.GFF3ParserTest [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.004 s -- in com.affymetrix.genometry.parsers.GFF3ParserTest [INFO] Running com.affymetrix.genometry.parsers.BpsParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.050 s -- in com.affymetrix.genometry.parsers.BpsParserTest [INFO] Running com.affymetrix.genometry.parsers.BrsParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s -- in com.affymetrix.genometry.parsers.BrsParserTest [INFO] Running com.affymetrix.genometry.parsers.TwoBitNewTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.362 s -- in com.affymetrix.genometry.parsers.TwoBitNewTest [INFO] Running com.affymetrix.genometry.parsers.NibbleFileParserTest in NibbleIterator.stringToNibbles(), start >= end NOT YET IMPLEMENTED in NibbleIterator.stringToNibbles(), start >= end NOT YET IMPLEMENTED [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.392 s -- in com.affymetrix.genometry.parsers.NibbleFileParserTest [INFO] Running com.affymetrix.genometry.parsers.NibbleResiduesParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s -- in com.affymetrix.genometry.parsers.NibbleResiduesParserTest [INFO] Running com.affymetrix.genometry.util.IgbStringUtilsTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.124 s -- in com.affymetrix.genometry.util.IgbStringUtilsTest [INFO] Running com.affymetrix.genometry.util.SeqUtilsTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s -- in com.affymetrix.genometry.util.SeqUtilsTest [INFO] Running com.affymetrix.genometry.BioSeqTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s -- in com.affymetrix.genometry.BioSeqTest [INFO] Running com.affymetrix.genometry.GFF3SymTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 s -- in com.affymetrix.genometry.GFF3SymTest [INFO] Running com.affymetrix.genometry.comparator.SeqSymIdComparatorTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s -- in com.affymetrix.genometry.comparator.SeqSymIdComparatorTest [INFO] Running com.affymetrix.genometry.NibbleBioSeqTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s -- in com.affymetrix.genometry.NibbleBioSeqTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 76, Failures: 0, Errors: 0, Skipped: 6 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ genometry --- [WARNING] Bundle org.lorainelab.igb:genometry:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/genometry/target/genometry-10.0.0.jar [INFO] Writing manifest: /build/core/genometry/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ genometry --- [INFO] Installing /build/core/genometry/pom.xml to /root/.m2/repository/org/lorainelab/igb/genometry/10.0.0/genometry-10.0.0.pom [INFO] Installing /build/core/genometry/target/genometry-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/genometry/10.0.0/genometry-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ genometry --- [INFO] Installing org/lorainelab/igb/genometry/10.0.0/genometry-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ genometry --- [INFO] Configured Artifact: org.lorainelab.igb:genometry:10.0.0:jar [INFO] Copying genometry-10.0.0.jar to /build/bundles/genometry-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:igb-preferences >----------------- [INFO] Building Core - Preferences 10.0.0 [9/57] [INFO] from core/igb-preferences/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom Downloading from central: https://repo.maven.apache.org/maven2/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom Progress (1): 9.4 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/google/code/gson/gson/2.10.1/gson-2.10.1.pom (9.4 kB at 2.3 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom Downloading from central: https://repo.maven.apache.org/maven2/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom Progress (1): 13 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/google/code/gson/gson-parent/2.10.1/gson-parent-2.10.1.pom (13 kB at 4.2 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar Downloading from repo2: https://maven.bioviz.org/repo2/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar Downloading from repo3: https://maven.bioviz.org/repo3/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar Downloading from central: https://repo.maven.apache.org/maven2/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar Progress (1): 16/283 kB Progress (1): 33/283 kB Progress (1): 49/283 kB Progress (1): 66/283 kB Progress (1): 82/283 kB Progress (1): 98/283 kB Progress (1): 115/283 kB Progress (1): 131/283 kB Progress (1): 147/283 kB Progress (1): 164/283 kB Progress (1): 180/283 kB Progress (1): 197/283 kB Progress (1): 213/283 kB Progress (1): 229/283 kB Progress (1): 246/283 kB Progress (1): 262/283 kB Progress (1): 279/283 kB Progress (1): 283 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/google/code/gson/gson/2.10.1/gson-2.10.1.jar (283 kB at 20 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igb-preferences --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igb-preferences --- [INFO] Changes detected - recompiling the module! :source [INFO] Compiling 8 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igb-preferences --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igb-preferences --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igb-preferences --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.lorainelab.igb.preferences.IgbPreferencesParseTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.773 s -- in com.lorainelab.igb.preferences.IgbPreferencesParseTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igb-preferences --- [WARNING] Bundle org.lorainelab.igb:igb-preferences:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/igb-preferences/target/igb-preferences-10.0.0.jar [INFO] Writing manifest: /build/core/igb-preferences/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igb-preferences --- [INFO] Installing /build/core/igb-preferences/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-preferences/10.0.0/igb-preferences-10.0.0.pom [INFO] Installing /build/core/igb-preferences/target/igb-preferences-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igb-preferences/10.0.0/igb-preferences-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igb-preferences --- [INFO] Installing org/lorainelab/igb/igb-preferences/10.0.0/igb-preferences-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igb-preferences --- [INFO] Configured Artifact: org.lorainelab.igb:igb-preferences:10.0.0:jar [INFO] Copying igb-preferences-10.0.0.jar to /build/bundles/igb-preferences-10.0.0.jar [INFO] [INFO] -------------------< org.lorainelab.igb:igbSwingExt >------------------- [INFO] Building Core - IGB Swing Extensions 10.0.0 [10/57] [INFO] from core/igb-swing-ext/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igbSwingExt --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/core/igb-swing-ext/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igbSwingExt --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 41 source files with javac [debug target 21] to target/classes [INFO] /build/core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/JRPComboBox.java: Some input files use unchecked or unsafe operations. [INFO] /build/core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/JRPComboBox.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- bundle:5.1.9:manifest (bundle-manifest) @ igbSwingExt --- [INFO] No MANIFEST.MF file found, generating manifest. [WARNING] Manifest org.lorainelab.igb:igbSwingExt:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Writing manifest: /build/core/igb-swing-ext/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igbSwingExt --- [INFO] skip non existing resourceDirectory /build/core/igb-swing-ext/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igbSwingExt --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igbSwingExt --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igbSwingExt --- [WARNING] Bundle org.lorainelab.igb:igbSwingExt:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/igb-swing-ext/target/igbSwingExt-10.0.0.jar [INFO] Writing manifest: /build/core/igb-swing-ext/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igbSwingExt --- [INFO] Installing /build/core/igb-swing-ext/pom.xml to /root/.m2/repository/org/lorainelab/igb/igbSwingExt/10.0.0/igbSwingExt-10.0.0.pom [INFO] Installing /build/core/igb-swing-ext/target/igbSwingExt-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igbSwingExt/10.0.0/igbSwingExt-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igbSwingExt --- [INFO] Installing org/lorainelab/igb/igbSwingExt/10.0.0/igbSwingExt-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igbSwingExt --- [INFO] Configured Artifact: org.lorainelab.igb:igbSwingExt:10.0.0:jar [INFO] Copying igbSwingExt-10.0.0.jar to /build/bundles/igbSwingExt-10.0.0.jar [INFO] [INFO] -------------< org.lorainelab.igb:igb-genoviz-extensions >-------------- [INFO] Building Core - Genoviz Extensions 10.0.0 [11/57] [INFO] from core/igb-genoviz-ext/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igb-genoviz-extensions --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igb-genoviz-extensions --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 10 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igb-genoviz-extensions --- [INFO] skip non existing resourceDirectory /build/core/igb-genoviz-ext/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igb-genoviz-extensions --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igb-genoviz-extensions --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igb-genoviz-extensions --- [WARNING] Bundle org.lorainelab.igb:igb-genoviz-extensions:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/igb-genoviz-ext/target/igb-genoviz-extensions-10.0.0.jar [INFO] Writing manifest: /build/core/igb-genoviz-ext/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igb-genoviz-extensions --- [INFO] Installing /build/core/igb-genoviz-ext/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-genoviz-extensions/10.0.0/igb-genoviz-extensions-10.0.0.pom [INFO] Installing /build/core/igb-genoviz-ext/target/igb-genoviz-extensions-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igb-genoviz-extensions/10.0.0/igb-genoviz-extensions-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igb-genoviz-extensions --- [INFO] Installing org/lorainelab/igb/igb-genoviz-extensions/10.0.0/igb-genoviz-extensions-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igb-genoviz-extensions --- [INFO] Configured Artifact: org.lorainelab.igb:igb-genoviz-extensions:10.0.0:jar [INFO] Copying igb-genoviz-extensions-10.0.0.jar to /build/bundles/igb-genoviz-extensions-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:igb-services >------------------- [INFO] Building Core - IGB Services API 10.0.0 [12/57] [INFO] from core/igb-services-api/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igb-services --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igb-services --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 20 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igb-services --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igb-services --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igb-services --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igb-services --- [WARNING] Bundle org.lorainelab.igb:igb-services:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/igb-services-api/target/igb-services-10.0.0.jar [INFO] Writing manifest: /build/core/igb-services-api/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igb-services --- [INFO] Installing /build/core/igb-services-api/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-services/10.0.0/igb-services-10.0.0.pom [INFO] Installing /build/core/igb-services-api/target/igb-services-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igb-services/10.0.0/igb-services-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igb-services --- [INFO] Installing org/lorainelab/igb/igb-services/10.0.0/igb-services-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igb-services --- [INFO] Configured Artifact: org.lorainelab.igb:igb-services:10.0.0:jar [INFO] Copying igb-services-10.0.0.jar to /build/bundles/igb-services-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:frameManager >------------------- [INFO] Building Core - Frame Manager 10.0.0 [13/57] [INFO] from core/frameManager/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom Downloading from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom Progress (1): 855 B Downloaded from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.pom (855 B at 171 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom Downloading from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom Progress (1): 8.9 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-parent/5.2/miglayout-parent-5.2.pom (8.9 kB at 3.0 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom Downloading from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom Progress (1): 633 B Downloaded from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.pom (633 B at 158 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar Downloading from repo1: https://maven.bioviz.org/repo1/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar Downloading from repo2: https://maven.bioviz.org/repo2/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar Downloading from repo2: https://maven.bioviz.org/repo2/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar Downloading from repo3: https://maven.bioviz.org/repo3/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar Downloading from repo3: https://maven.bioviz.org/repo3/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar Downloading from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar Progress (1): 16/22 kB Progress (1): 22 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-swing/5.2/miglayout-swing-5.2.jar (22 kB at 5.6 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar Progress (1): 16/107 kB Progress (1): 33/107 kB Progress (1): 49/107 kB Progress (1): 66/107 kB Progress (1): 82/107 kB Progress (1): 98/107 kB Progress (1): 107 kB Downloaded from central: https://repo.maven.apache.org/maven2/com/miglayout/miglayout-core/5.2/miglayout-core-5.2.jar (107 kB at 12 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ frameManager --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ frameManager --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ frameManager --- [INFO] skip non existing resourceDirectory /build/core/frameManager/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ frameManager --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ frameManager --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ frameManager --- [WARNING] Bundle org.lorainelab.igb:frameManager:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/frameManager/target/frameManager-10.0.0.jar [INFO] Writing manifest: /build/core/frameManager/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ frameManager --- [INFO] Installing /build/core/frameManager/pom.xml to /root/.m2/repository/org/lorainelab/igb/frameManager/10.0.0/frameManager-10.0.0.pom [INFO] Installing /build/core/frameManager/target/frameManager-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/frameManager/10.0.0/frameManager-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ frameManager --- [INFO] Installing org/lorainelab/igb/frameManager/10.0.0/frameManager-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ frameManager --- [INFO] Configured Artifact: org.lorainelab.igb:frameManager:10.0.0:jar [INFO] Copying frameManager-10.0.0.jar to /build/bundles/frameManager-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:window-service >------------------ [INFO] Building Core - Window Service 10.0.0 [14/57] [INFO] from core/window-service/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ window-service --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ window-service --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 13 source files with javac [debug target 21] to target/classes [INFO] /build/core/window-service/src/main/java/com/affymetrix/igb/window/service/def/WindowServiceDefaultImpl.java: /build/core/window-service/src/main/java/com/affymetrix/igb/window/service/def/WindowServiceDefaultImpl.java uses or overrides a deprecated API. [INFO] /build/core/window-service/src/main/java/com/affymetrix/igb/window/service/def/WindowServiceDefaultImpl.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ window-service --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ window-service --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ window-service --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ window-service --- [WARNING] Bundle org.lorainelab.igb:window-service:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/window-service/target/window-service-10.0.0.jar [INFO] Writing manifest: /build/core/window-service/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ window-service --- [INFO] Installing /build/core/window-service/pom.xml to /root/.m2/repository/org/lorainelab/igb/window-service/10.0.0/window-service-10.0.0.pom [INFO] Installing /build/core/window-service/target/window-service-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/window-service/10.0.0/window-service-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ window-service --- [INFO] Installing org/lorainelab/igb/window-service/10.0.0/window-service-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ window-service --- [INFO] Configured Artifact: org.lorainelab.igb:window-service:10.0.0:jar [INFO] Copying window-service-10.0.0.jar to /build/bundles/window-service-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:igb-javafx-util >----------------- [INFO] Building Core - JavaFX Utilities 10.0.0 [15/57] [INFO] from core/igb-javafx-util/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igb-javafx-util --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/core/igb-javafx-util/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igb-javafx-util --- [INFO] Changes detected - recompiling the module! :source [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igb-javafx-util --- [INFO] skip non existing resourceDirectory /build/core/igb-javafx-util/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igb-javafx-util --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igb-javafx-util --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igb-javafx-util --- [WARNING] Bundle org.lorainelab.igb:igb-javafx-util:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/igb-javafx-util/target/igb-javafx-util-10.0.0.jar [INFO] Writing manifest: /build/core/igb-javafx-util/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igb-javafx-util --- [INFO] Installing /build/core/igb-javafx-util/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-javafx-util/10.0.0/igb-javafx-util-10.0.0.pom [INFO] Installing /build/core/igb-javafx-util/target/igb-javafx-util-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igb-javafx-util/10.0.0/igb-javafx-util-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igb-javafx-util --- [INFO] Installing org/lorainelab/igb/igb-javafx-util/10.0.0/igb-javafx-util-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igb-javafx-util --- [INFO] Configured Artifact: org.lorainelab.igb:igb-javafx-util:10.0.0:jar [INFO] Copying igb-javafx-util-10.0.0.jar to /build/bundles/igb-javafx-util-10.0.0.jar [INFO] [INFO] -----------< org.lorainelab.igb:org.lorainelab.igb.menu.api >----------- [INFO] Building Core - Menu API 10.0.0 [16/57] [INFO] from core/menu-api/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ org.lorainelab.igb.menu.api --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/core/menu-api/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ org.lorainelab.igb.menu.api --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 13 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ org.lorainelab.igb.menu.api --- [INFO] skip non existing resourceDirectory /build/core/menu-api/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ org.lorainelab.igb.menu.api --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ org.lorainelab.igb.menu.api --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ org.lorainelab.igb.menu.api --- [WARNING] Bundle org.lorainelab.igb:org.lorainelab.igb.menu.api:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/menu-api/target/org.lorainelab.igb.menu.api-10.0.0.jar [INFO] Writing manifest: /build/core/menu-api/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ org.lorainelab.igb.menu.api --- [INFO] Installing /build/core/menu-api/pom.xml to /root/.m2/repository/org/lorainelab/igb/org.lorainelab.igb.menu.api/10.0.0/org.lorainelab.igb.menu.api-10.0.0.pom [INFO] Installing /build/core/menu-api/target/org.lorainelab.igb.menu.api-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/org.lorainelab.igb.menu.api/10.0.0/org.lorainelab.igb.menu.api-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ org.lorainelab.igb.menu.api --- [INFO] Installing org/lorainelab/igb/org.lorainelab.igb.menu.api/10.0.0/org.lorainelab.igb.menu.api-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ org.lorainelab.igb.menu.api --- [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.menu.api:10.0.0:jar [INFO] Copying org.lorainelab.igb.menu.api-10.0.0.jar to /build/bundles/org.lorainelab.igb.menu.api-10.0.0.jar [INFO] [INFO] --------------< org.lorainelab.igb:context-menu-service >--------------- [INFO] Building Core - Context Menu Service 10.0.0 [17/57] [INFO] from core/context-menu-service/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ context-menu-service --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/core/context-menu-service/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ context-menu-service --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ context-menu-service --- [INFO] skip non existing resourceDirectory /build/core/context-menu-service/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ context-menu-service --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ context-menu-service --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ context-menu-service --- [WARNING] Bundle org.lorainelab.igb:context-menu-service:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/context-menu-service/target/context-menu-service-10.0.0.jar [INFO] Writing manifest: /build/core/context-menu-service/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ context-menu-service --- [INFO] Installing /build/core/context-menu-service/pom.xml to /root/.m2/repository/org/lorainelab/igb/context-menu-service/10.0.0/context-menu-service-10.0.0.pom [INFO] Installing /build/core/context-menu-service/target/context-menu-service-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/context-menu-service/10.0.0/context-menu-service-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ context-menu-service --- [INFO] Installing org/lorainelab/igb/context-menu-service/10.0.0/context-menu-service-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ context-menu-service --- [INFO] Configured Artifact: org.lorainelab.igb:context-menu-service:10.0.0:jar [INFO] Copying context-menu-service-10.0.0.jar to /build/bundles/context-menu-service-10.0.0.jar [INFO] [INFO] -----------------------< org.lorainelab.igb:igb >----------------------- [INFO] Building Core - IGB 10.0.0 [18/57] [INFO] from core/igb/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/4.9.10/git-commit-id-plugin-4.9.10.pom Progress (1): 12 kB Downloaded from central: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/4.9.10/git-commit-id-plugin-4.9.10.pom (12 kB at 3.0 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin-parent/4.9.10/git-commit-id-plugin-parent-4.9.10.pom Progress (1): 12 kB Downloaded from central: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin-parent/4.9.10/git-commit-id-plugin-parent-4.9.10.pom (12 kB at 4.1 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/4.9.10/git-commit-id-plugin-4.9.10.jar Progress (1): 16/40 kB Progress (1): 33/40 kB Progress (1): 40 kB Downloaded from central: https://repo.maven.apache.org/maven2/pl/project13/maven/git-commit-id-plugin/4.9.10/git-commit-id-plugin-4.9.10.jar (40 kB at 13 MB/s) [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/com/boxysystems/jgoogleanalytics/0.4/jgoogleanalytics-0.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/com/boxysystems/jgoogleanalytics/0.4/jgoogleanalytics-0.4.pom Progress (1): 465 B Downloaded from repo2: https://maven.bioviz.org/repo2/com/boxysystems/jgoogleanalytics/0.4/jgoogleanalytics-0.4.pom (465 B at 21 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom Downloading from central: https://repo.maven.apache.org/maven2/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom Progress (1): 1.1 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/freehep/freehep-graphicsio-svg/2.4/freehep-graphicsio-svg-2.4.pom (1.1 kB at 364 kB/s) Downloading from repo1: 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https://maven.bioviz.org/repo1/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom Downloading from central: https://repo.maven.apache.org/maven2/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom Progress (1): 6.9 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/freehep/freehep-io/2.2.2/freehep-io-2.2.2.pom (6.9 kB at 1.7 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/junit/junit/4.10/junit-4.10.pom Downloading from repo2: https://maven.bioviz.org/repo2/junit/junit/4.10/junit-4.10.pom Downloading from repo3: https://maven.bioviz.org/repo3/junit/junit/4.10/junit-4.10.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/junit/junit/4.10/junit-4.10.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/junit/junit/4.10/junit-4.10.pom Downloading from central: https://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.pom Progress (1): 2.3 kB Downloaded from central: https://repo.maven.apache.org/maven2/junit/junit/4.10/junit-4.10.pom (2.3 kB at 782 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom Downloading from central: https://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom Progress (1): 481 B Downloaded from central: https://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.pom (481 B at 160 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom Downloading from central: https://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom Progress (1): 5.9 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/hamcrest/hamcrest-parent/1.1/hamcrest-parent-1.1.pom (5.9 kB at 1.5 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/freehep/freehep-graphicsio/2.4/freehep-graphicsio-2.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/freehep/freehep-graphicsio/2.4/freehep-graphicsio-2.4.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/freehep/freehep-graphicsio/2.4/freehep-graphicsio-2.4.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/freehep/freehep-graphicsio/2.4/freehep-graphicsio-2.4.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/freehep/freehep-graphicsio/2.4/freehep-graphicsio-2.4.pom Downloading from central: 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(1): 2.5/2.8 MB Progress (1): 2.5/2.8 MB Progress (1): 2.6/2.8 MB Progress (1): 2.6/2.8 MB Progress (1): 2.6/2.8 MB Progress (1): 2.6/2.8 MB Progress (1): 2.6/2.8 MB Progress (1): 2.6/2.8 MB Progress (1): 2.7/2.8 MB Progress (1): 2.7/2.8 MB Progress (1): 2.7/2.8 MB Progress (1): 2.7/2.8 MB Progress (1): 2.7/2.8 MB Progress (1): 2.7/2.8 MB Progress (1): 2.8/2.8 MB Progress (1): 2.8/2.8 MB Progress (1): 2.8/2.8 MB Progress (1): 2.8/2.8 MB Progress (1): 2.8 MB Downloaded from central: https://repo.maven.apache.org/maven2/org/eclipse/jgit/org.eclipse.jgit/5.12.0.202106070339-r/org.eclipse.jgit-5.12.0.202106070339-r.jar (2.8 MB at 12 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igb --- [INFO] Copying 12 resources from src/main/resources to target/classes [INFO] Copying 48 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igb --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 336 source files with javac [debug target 21] to target/classes [WARNING] unknown enum constant jakarta.xml.bind.annotation.XmlAccessType.FIELD reason: class file for jakarta.xml.bind.annotation.XmlAccessType not found [WARNING] unknown enum constant jakarta.xml.bind.annotation.XmlAccessType.FIELD [INFO] /build/core/igb/src/main/java/com/affymetrix/igb/view/SeqMapViewMouseListener.java: Some input files use or override a deprecated API. [INFO] /build/core/igb/src/main/java/com/affymetrix/igb/view/SeqMapViewMouseListener.java: Recompile with -Xlint:deprecation for details. [INFO] /build/core/igb/src/main/java/com/affymetrix/igb/prefs/AnnotationLabelOptions.java: Some input files use unchecked or unsafe operations. [INFO] /build/core/igb/src/main/java/com/affymetrix/igb/prefs/AnnotationLabelOptions.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igb --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igb --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igb --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igb --- [WARNING] Bundle org.lorainelab.igb:igb:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [WARNING] Bundle org.lorainelab.igb:igb:bundle:10.0.0 : Export com.affymetrix.igb.shared, has 2, private references [com.affymetrix.igb.action, com.affymetrix.igb.tiers] [WARNING] Bundle org.lorainelab.igb:igb:bundle:10.0.0 : Export com.affymetrix.igb.view.load, has 2, private references [com.affymetrix.igb.tiers, com.affymetrix.igb.view] [WARNING] Bundle org.lorainelab.igb:igb:bundle:10.0.0 : Export com.affymetrix.igb.view.factories, has 3, private references [com.affymetrix.igb.services.registry, com.affymetrix.igb.view, com.affymetrix.igb.view.layout] [WARNING] Bundle org.lorainelab.igb:igb:bundle:10.0.0 : Export com.affymetrix.igb.glyph, has 1, private references [com.affymetrix.igb.view] [INFO] Building bundle: /build/core/igb/target/igb-10.0.0.jar [INFO] Writing manifest: /build/core/igb/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igb --- [INFO] Installing /build/core/igb/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb/10.0.0/igb-10.0.0.pom [INFO] Installing /build/core/igb/target/igb-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igb/10.0.0/igb-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igb --- [INFO] Installing org/lorainelab/igb/igb/10.0.0/igb-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igb --- [INFO] Configured Artifact: org.lorainelab.igb:igb:10.0.0:jar [INFO] Copying igb-10.0.0.jar to /build/bundles/igb-10.0.0.jar [INFO] [INFO] ---------------< org.lorainelab.igb:shared-lib-wrapper >---------------- [INFO] Building Core - Bundle wrapper, deployer 10.0.0 [19/57] [INFO] from core/shared-lib-wrapper/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/fi/iki/elonen/NanoHTTPD/2.0.5/NanoHTTPD-2.0.5.pom Downloading from repo2: https://maven.bioviz.org/repo2/fi/iki/elonen/NanoHTTPD/2.0.5/NanoHTTPD-2.0.5.pom Progress (1): 458 B Downloaded from repo2: https://maven.bioviz.org/repo2/fi/iki/elonen/NanoHTTPD/2.0.5/NanoHTTPD-2.0.5.pom (458 B at 13 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/fi/iki/elonen/NanoHTTPD/2.0.5/NanoHTTPD-2.0.5.jar Downloading from repo2: https://maven.bioviz.org/repo2/fi/iki/elonen/NanoHTTPD/2.0.5/NanoHTTPD-2.0.5.jar Progress (1): 16/48 kB Progress (1): 33/48 kB Progress (1): 48 kB Downloaded from repo2: https://maven.bioviz.org/repo2/fi/iki/elonen/NanoHTTPD/2.0.5/NanoHTTPD-2.0.5.jar (48 kB at 1.3 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ shared-lib-wrapper --- [INFO] skip non existing resourceDirectory /build/core/shared-lib-wrapper/src/main/java [INFO] skip non existing resourceDirectory /build/core/shared-lib-wrapper/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ shared-lib-wrapper --- [INFO] No sources to compile [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ shared-lib-wrapper --- [INFO] skip non existing resourceDirectory /build/core/shared-lib-wrapper/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ shared-lib-wrapper --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ shared-lib-wrapper --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ shared-lib-wrapper --- [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Split package, multiple jars provide the same package:org/hamcrest Use Import/Export Package directive -split-package:=(merge-first|merge-last|error|first) to get rid of this warning Package found in [Jar:junit, Jar:hamcrest-core] Class path [Jar:txw2, Jar:jdom, Jar:commons-net, Jar:image4j, Jar:colt, Jar:concurrent, Jar:freehep-graphicsio-svg, Jar:freehep-graphics2d, Jar:junit, Jar:hamcrest-core, Jar:freehep-graphicsio, Jar:freehep-io, Jar:freehep-graphicsio-tests, Jar:freehep-graphicsbase, Jar:swing-layout, Jar:swingx-all, Jar:miglayout-core, Jar:miglayout-swing, Jar:jgoogleanalytics, Jar:http-request, Jar:NanoHTTPD] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Split package, multiple jars provide the same package:org/hamcrest/core Use Import/Export Package directive -split-package:=(merge-first|merge-last|error|first) to get rid of this warning Package found in [Jar:junit, Jar:hamcrest-core] Class path [Jar:txw2, Jar:jdom, Jar:commons-net, Jar:image4j, Jar:colt, Jar:concurrent, Jar:freehep-graphicsio-svg, Jar:freehep-graphics2d, Jar:junit, Jar:hamcrest-core, Jar:freehep-graphicsio, Jar:freehep-io, Jar:freehep-graphicsio-tests, Jar:freehep-graphicsbase, Jar:swing-layout, Jar:swingx-all, Jar:miglayout-core, Jar:miglayout-swing, Jar:jgoogleanalytics, Jar:http-request, Jar:NanoHTTPD] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Split package, multiple jars provide the same package:org/hamcrest/internal Use Import/Export Package directive -split-package:=(merge-first|merge-last|error|first) to get rid of this warning Package found in [Jar:junit, Jar:hamcrest-core] Class path [Jar:txw2, Jar:jdom, Jar:commons-net, Jar:image4j, Jar:colt, Jar:concurrent, Jar:freehep-graphicsio-svg, Jar:freehep-graphics2d, Jar:junit, Jar:hamcrest-core, Jar:freehep-graphicsio, Jar:freehep-io, Jar:freehep-graphicsio-tests, Jar:freehep-graphicsbase, Jar:swing-layout, Jar:swingx-all, Jar:miglayout-core, Jar:miglayout-swing, Jar:jgoogleanalytics, Jar:http-request, Jar:NanoHTTPD] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Unused Export-Package instructions: [affymetrix.calvin.*, affymetrix.fusion.*, affymetrix.gcos.*, org.jdom.*, org.jdesktop.swingx.*, com.boxysystems.jgoogleanalytics.*] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export cern.colt.matrix.doublealgo, has 3, private references [cern.jet.random.engine, hep.aida, hep.aida.bin] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export org.freehep.graphicsbase.util, has 1, private references [junit.framework] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export org.freehep.graphicsio.test, has 1, private references [junit.framework] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export-Package duplicate package name (org.jdesktop.swingx) that uses the default version because no version is specified (10.0.0). Remove duplicate package or add an explicit version to it. [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export-Package duplicate package name (com.sun.xml.txw2) that uses the default version because no version is specified (10.0.0). Remove duplicate package or add an explicit version to it. [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export-Package duplicate package name (com.sun.xml.txw2.annotation) that uses the default version because no version is specified (10.0.0). Remove duplicate package or add an explicit version to it. [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:10.0.0 : Export-Package duplicate package name (com.sun.xml.txw2.output) that uses the default version because no version is specified (10.0.0). Remove duplicate package or add an explicit version to it. [INFO] Building bundle: /build/core/shared-lib-wrapper/target/shared-lib-wrapper-10.0.0.jar [INFO] Writing manifest: /build/core/shared-lib-wrapper/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ shared-lib-wrapper --- [INFO] Installing /build/core/shared-lib-wrapper/pom.xml to /root/.m2/repository/org/lorainelab/igb/shared-lib-wrapper/10.0.0/shared-lib-wrapper-10.0.0.pom [INFO] Installing /build/core/shared-lib-wrapper/target/shared-lib-wrapper-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/shared-lib-wrapper/10.0.0/shared-lib-wrapper-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ shared-lib-wrapper --- [INFO] Installing org/lorainelab/igb/shared-lib-wrapper/10.0.0/shared-lib-wrapper-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ shared-lib-wrapper --- [INFO] Configured Artifact: com.google.guava:guava:32.1.1-jre:jar [INFO] Configured Artifact: com.google.guava:failureaccess:1.0.1:jar [INFO] Configured Artifact: org.apache.commons:commons-lang3:3.12.0:jar [INFO] Configured Artifact: org.apache.commons:commons-csv:1.10.0:jar [INFO] Configured Artifact: commons-io:commons-io:2.11.0:jar [INFO] Configured Artifact: com.affymetrix:genoviz:1.1.9:jar [INFO] Configured Artifact: org.lorainelab.igb:shared-lib-wrapper:10.0.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.main:7.0.5:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.scr:2.2.6:jar Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom Progress (1): 15 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.pom (15 kB at 675 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.scr/2.2.6/org.apache.felix.scr-2.2.6.jar Progress (1): 16/403 kB Progress (1): 32/403 kB Progress (1): 49/403 kB Progress (1): 65/403 kB Progress (1): 81/403 kB Progress (1): 98/403 kB Progress (1): 114/403 kB Progress (1): 131/403 kB Progress (1): 147/403 kB Progress (1): 163/403 kB Progress (1): 180/403 kB Progress (1): 196/403 kB Progress (1): 212/403 kB Progress (1): 229/403 kB Progress (1): 245/403 kB Progress (1): 262/403 kB Progress (1): 278/403 kB Progress (1): 294/403 kB Progress (1): 311/403 kB Progress (1): 327/403 kB Progress (1): 344/403 kB Progress (1): 360/403 kB Progress (1): 376/403 kB 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(1): 65/163 kB Progress (1): 81/163 kB Progress (1): 98/163 kB Progress (1): 114/163 kB Progress (1): 131/163 kB Progress (1): 147/163 kB Progress (1): 163 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.configadmin/1.9.26/org.apache.felix.configadmin-1.9.26.jar (163 kB at 18 MB/s) [INFO] Configured Artifact: org.apache.felix:org.apache.felix.fileinstall:3.7.4:jar Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.fileinstall/3.7.4/org.apache.felix.fileinstall-3.7.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.fileinstall/3.7.4/org.apache.felix.fileinstall-3.7.4.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.fileinstall/3.7.4/org.apache.felix.fileinstall-3.7.4.pom Downloading from maven-releases: 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[INFO] Configured Artifact: com.github.kevinsawicki:http-request:6.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.http.servlet-api:?:jar Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.http.servlet-api/2.1.0/org.apache.felix.http.servlet-api-2.1.0.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.http.servlet-api/2.1.0/org.apache.felix.http.servlet-api-2.1.0.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.http.servlet-api/2.1.0/org.apache.felix.http.servlet-api-2.1.0.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.http.servlet-api/2.1.0/org.apache.felix.http.servlet-api-2.1.0.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.http.servlet-api/2.1.0/org.apache.felix.http.servlet-api-2.1.0.pom Downloading from 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org.apache.felix:org.apache.felix.webconsole:4.8.8:jar Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom Progress (1): 16/19 kB Progress (1): 19 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.pom (19 kB at 4.8 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.jar Downloading from central: 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https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.webconsole/4.8.8/org.apache.felix.webconsole-4.8.8.jar (541 kB at 27 MB/s) [INFO] Configured Artifact: commons-fileupload:commons-fileupload:1.5:jar Downloading from repo1: https://maven.bioviz.org/repo1/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom Downloading from repo2: https://maven.bioviz.org/repo2/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom Downloading from repo3: https://maven.bioviz.org/repo3/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom Downloading from central: https://repo.maven.apache.org/maven2/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom Progress (1): 16 kB Downloaded from central: https://repo.maven.apache.org/maven2/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.pom (16 kB at 5.4 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar Downloading from repo2: https://maven.bioviz.org/repo2/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar Downloading from repo3: https://maven.bioviz.org/repo3/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar Downloading from central: https://repo.maven.apache.org/maven2/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar Progress (1): 16/74 kB Progress (1): 33/74 kB Progress (1): 37/74 kB Progress (1): 53/74 kB Progress (1): 69/74 kB Progress (1): 74 kB Downloaded from central: https://repo.maven.apache.org/maven2/commons-fileupload/commons-fileupload/1.5/commons-fileupload-1.5.jar (74 kB at 25 MB/s) [INFO] Configured Artifact: org.apache.felix:org.apache.felix.eventadmin:1.6.4:jar Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom Progress (1): 10 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.pom (10 kB at 3.4 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar Progress (1): 16/84 kB Progress (1): 33/84 kB Progress (1): 49/84 kB Progress (1): 66/84 kB Progress (1): 82/84 kB Progress (1): 84 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/felix/org.apache.felix.eventadmin/1.6.4/org.apache.felix.eventadmin-1.6.4.jar (84 kB at 17 MB/s) [INFO] Copying guava-32.1.1-jre.jar to /build/bundles/guava-32.1.1-jre.jar [INFO] Copying failureaccess-1.0.1.jar to /build/bundles/failureaccess-1.0.1.jar [INFO] Copying commons-lang3-3.12.0.jar to /build/bundles/commons-lang3-3.12.0.jar [INFO] Copying commons-csv-1.10.0.jar to /build/bundles/commons-csv-1.10.0.jar [INFO] Copying commons-io-2.11.0.jar to /build/bundles/commons-io-2.11.0.jar [INFO] Copying genoviz-1.1.9.jar to /build/bundles/genoviz-1.1.9.jar [INFO] Copying shared-lib-wrapper-10.0.0.jar to /build/bundles/shared-lib-wrapper-10.0.0.jar [INFO] Copying org.apache.felix.main-7.0.5.jar to /build/bundles/felix.jar [INFO] Copying org.apache.felix.scr-2.2.6.jar to /build/bundles/org.apache.felix.scr-2.2.6.jar [INFO] Copying org.osgi.service.log-1.5.0.jar to /build/bundles/org.osgi.service.log-1.5.0.jar [INFO] Copying org.osgi.service.component-1.5.1.jar to /build/bundles/org.osgi.service.component-1.5.1.jar [INFO] Copying org.osgi.service.component.annotations-1.5.1.jar to /build/bundles/org.osgi.service.component.annotations-1.5.1.jar [INFO] Copying org.apache.felix.bundlerepository-2.0.10.jar to /build/bundles/org.apache.felix.bundlerepository-2.0.10.jar [INFO] Copying bigwig-2.0.1.jar to /build/bundles/bigwig-2.0.1.jar [INFO] Copying commons-compress-1.23.0.jar to /build/bundles/commons-compress-1.23.0.jar [INFO] Copying commons-codec-1.15.jar to /build/bundles/commons-codec-1.15.jar [INFO] Copying commons-pool-1.6.jar to /build/bundles/commons-pool-1.6.jar [INFO] Copying commons-logging-1.2.jar to /build/bundles/commons-logging-1.2.jar [INFO] Copying commons-jexl-2.1.1.jar to /build/bundles/commons-jexl-2.1.1.jar [INFO] Copying istack-commons-runtime-3.0.12.jar to /build/bundles/istack-commons-runtime-3.0.12.jar [INFO] Copying jide-ultimate-jakarta-3.5.15.jar to /build/bundles/jide-ultimate-jakarta-3.5.15.jar [INFO] Copying gson-2.10.1.jar to /build/bundles/gson-2.10.1.jar [INFO] Copying slf4j-api-1.7.36.jar to /build/bundles/slf4j-api-1.7.36.jar [INFO] Copying logback-core-1.2.12.jar to /build/bundles/logback-core-1.2.12.jar [INFO] Copying logback-classic-1.2.12.jar to /build/bundles/logback-classic-1.2.12.jar [INFO] Copying htsjdk-igb-3.0.5.jar to /build/bundles/htsjdk-igb-3.0.5.jar [INFO] Copying org.apache.felix.http.base-5.1.2.jar to /build/bundles/org.apache.felix.http.base-5.1.2.jar [INFO] Copying org.apache.felix.configadmin-1.9.26.jar to /build/bundles/org.apache.felix.configadmin-1.9.26.jar [INFO] Copying org.apache.felix.fileinstall-3.7.4.jar to /build/bundles/org.apache.felix.fileinstall-3.7.4.jar [INFO] Copying http-request-6.0.jar to /build/bundles/http-request-6.0.jar [INFO] Copying org.apache.felix.http.servlet-api-2.1.0.jar to /build/bundles/org.apache.felix.http.servlet-api-2.1.0.jar [INFO] Copying org.apache.felix.http.jetty-5.1.4.jar to /build/bundles/org.apache.felix.http.jetty-5.1.4.jar [INFO] Copying org.apache.felix.webconsole-4.8.8.jar to /build/bundles/org.apache.felix.webconsole-4.8.8.jar [INFO] Copying commons-fileupload-1.5.jar to /build/bundles/commons-fileupload-1.5.jar [INFO] Copying org.apache.felix.eventadmin-1.6.4.jar to /build/bundles/org.apache.felix.eventadmin-1.6.4.jar [INFO] [INFO] -----------------< org.lorainelab.igb:logging-config >------------------ [INFO] Building Core - Logging Config 10.0.0 [20/57] [INFO] from core/logging-config/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ logging-config --- [INFO] skip non existing resourceDirectory /build/core/logging-config/src/main/java [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ logging-config --- [INFO] No sources to compile [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ logging-config --- [INFO] skip non existing resourceDirectory /build/core/logging-config/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ logging-config --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ logging-config --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ logging-config --- [WARNING] Bundle org.lorainelab.igb:logging-config:bundle:10.0.0 : Host ch.qos.logback.classic= for this fragment/require bundle cannot be found on the classpath [INFO] Building bundle: /build/core/logging-config/target/logging-config-10.0.0.jar [INFO] Writing manifest: /build/core/logging-config/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ logging-config --- [INFO] Installing /build/core/logging-config/pom.xml to /root/.m2/repository/org/lorainelab/igb/logging-config/10.0.0/logging-config-10.0.0.pom [INFO] Installing /build/core/logging-config/target/logging-config-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/logging-config/10.0.0/logging-config-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ logging-config --- [INFO] Installing org/lorainelab/igb/logging-config/10.0.0/logging-config-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ logging-config --- [INFO] Configured Artifact: org.lorainelab.igb:logging-config:10.0.0:jar [INFO] Copying logging-config-10.0.0.jar to /build/bundles/logging-config-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:weblinks >--------------------- [INFO] Building Core - Web Links 10.0.0 [21/57] [INFO] from core/weblinks/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ weblinks --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 5 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ weblinks --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 10 source files with javac [debug target 21] to target/classes [WARNING] unknown enum constant jakarta.xml.bind.annotation.XmlAccessType.FIELD reason: class file for jakarta.xml.bind.annotation.XmlAccessType not found [WARNING] unknown enum constant jakarta.xml.bind.annotation.XmlAccessType.FIELD [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ weblinks --- [INFO] skip non existing resourceDirectory /build/core/weblinks/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ weblinks --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ weblinks --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ weblinks --- [WARNING] Bundle org.lorainelab.igb:weblinks:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/weblinks/target/weblinks-10.0.0.jar [INFO] Writing manifest: /build/core/weblinks/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ weblinks --- [INFO] Installing /build/core/weblinks/pom.xml to /root/.m2/repository/org/lorainelab/igb/weblinks/10.0.0/weblinks-10.0.0.pom [INFO] Installing /build/core/weblinks/target/weblinks-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/weblinks/10.0.0/weblinks-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ weblinks --- [INFO] Installing org/lorainelab/igb/weblinks/10.0.0/weblinks-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ weblinks --- [INFO] Configured Artifact: org.lorainelab.igb:weblinks:10.0.0:jar [INFO] Copying weblinks-10.0.0.jar to /build/bundles/dynamic/weblinks-10.0.0.jar [INFO] [INFO] ----------------------< org.lorainelab.igb:cache >---------------------- [INFO] Building Plugin - Data caching GUI 10.0.0 [22/57] [INFO] from plugins/cache/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ cache --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/cache/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ cache --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/plugins/cache/src/main/java/org/lorainelab/igb/cache/disk/RemoteFileDiskCacheService.java: Some input files use or override a deprecated API. [INFO] /build/plugins/cache/src/main/java/org/lorainelab/igb/cache/disk/RemoteFileDiskCacheService.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ cache --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ cache --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 1.8] to target/test-classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] /build/plugins/cache/src/test/java/com/lorainelab/cache/disk/RemoteFileCacheServiceTest.java: /build/plugins/cache/src/test/java/com/lorainelab/cache/disk/RemoteFileCacheServiceTest.java uses or overrides a deprecated API. [INFO] /build/plugins/cache/src/test/java/com/lorainelab/cache/disk/RemoteFileCacheServiceTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ cache --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.lorainelab.cache.disk.RemoteFileCacheServiceTest [WARNING] Tests run: 8, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.502 s -- in com.lorainelab.cache.disk.RemoteFileCacheServiceTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 8, Failures: 0, Errors: 0, Skipped: 8 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ cache --- [WARNING] Bundle org.lorainelab.igb:cache:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/cache/target/cache-10.0.0.jar [INFO] Writing manifest: /build/plugins/cache/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ cache --- [INFO] Installing /build/plugins/cache/pom.xml to /root/.m2/repository/org/lorainelab/igb/cache/10.0.0/cache-10.0.0.pom [INFO] Installing /build/plugins/cache/target/cache-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/cache/10.0.0/cache-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ cache --- [INFO] Installing org/lorainelab/igb/cache/10.0.0/cache-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ cache --- [INFO] Configured Artifact: org.lorainelab.igb:cache:10.0.0:jar [INFO] Copying cache-10.0.0.jar to /build/bundles/dynamic/cache-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:quickload >-------------------- [INFO] Building Core - Quickload (data source) 10.0.0 [23/57] [INFO] from core/quickload/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ quickload --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ quickload --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 7 source files with javac [debug target 21] to target/classes [INFO] /build/core/quickload/src/main/java/org/lorainelab/igb/quickload/util/QuickloadUtils.java: /build/core/quickload/src/main/java/org/lorainelab/igb/quickload/util/QuickloadUtils.java uses or overrides a deprecated API. [INFO] /build/core/quickload/src/main/java/org/lorainelab/igb/quickload/util/QuickloadUtils.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ quickload --- [INFO] Copying 9 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ quickload --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ quickload --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.quickload.utils.AnnotsParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.624 s -- in org.lorainelab.igb.quickload.utils.AnnotsParserTest [INFO] Running org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest 15:57:29.526 [main] INFO org.lorainelab.igb.quickload.QuickloadDataProvider - Initializing Quickload Server file:/build/core/quickload/target/test-classes/quickload/ 15:57:29.546 [main] WARN org.lorainelab.igb.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from file:/build/core/quickload/target/test-classes/quickload/synonyms.txt 15:57:29.547 [main] WARN org.lorainelab.igb.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: file:/build/core/quickload/target/test-classes/quickload/species.txt [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.226 s -- in org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest [INFO] Running org.lorainelab.igb.quickload.utils.QuickloadUtilsTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 s -- in org.lorainelab.igb.quickload.utils.QuickloadUtilsTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ quickload --- [WARNING] Bundle org.lorainelab.igb:quickload:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/quickload/target/quickload-10.0.0.jar [INFO] Writing manifest: /build/core/quickload/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ quickload --- [INFO] Installing /build/core/quickload/pom.xml to /root/.m2/repository/org/lorainelab/igb/quickload/10.0.0/quickload-10.0.0.pom [INFO] Installing /build/core/quickload/target/quickload-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/quickload/10.0.0/quickload-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ quickload --- [INFO] Installing org/lorainelab/igb/quickload/10.0.0/quickload-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ quickload --- [INFO] Configured Artifact: org.lorainelab.igb:quickload:10.0.0:jar [INFO] Copying quickload-10.0.0.jar to /build/bundles/dynamic/quickload-10.0.0.jar [INFO] [INFO] -----------------------< org.lorainelab.igb:das >----------------------- [INFO] Building Core - DAS (data source) 10.0.0 [24/57] [INFO] from core/das/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ das --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/core/das/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ das --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 33 source files with javac [debug target 21] to target/classes [INFO] /build/core/das/src/main/java/org/lorainelab/igb/das/utils/DasServerUtils.java: Some input files use or override a deprecated API. [INFO] /build/core/das/src/main/java/org/lorainelab/igb/das/utils/DasServerUtils.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ das --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ das --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ das --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.lorainelab.das.DASFeatureParserTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.968 s -- in com.lorainelab.das.DASFeatureParserTest [INFO] Running com.lorainelab.das.DasDataProviderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.940 s -- in com.lorainelab.das.DasDataProviderTest [INFO] Running com.lorainelab.das.DasServerInfoTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.023 s -- in com.lorainelab.das.DasServerInfoTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 5 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ das --- [WARNING] Bundle org.lorainelab.igb:das:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/core/das/target/das-10.0.0.jar [INFO] Writing manifest: /build/core/das/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ das --- [INFO] Installing /build/core/das/pom.xml to /root/.m2/repository/org/lorainelab/igb/das/10.0.0/das-10.0.0.pom [INFO] Installing /build/core/das/target/das-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/das/10.0.0/das-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ das --- [INFO] Installing org/lorainelab/igb/das/10.0.0/das-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ das --- [INFO] Configured Artifact: org.lorainelab.igb:das:10.0.0:jar [INFO] Copying das-10.0.0.jar to /build/bundles/dynamic/das-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:apollo-library >------------------ [INFO] Building Plugin - Apollo Library 10.0.0 [25/57] [INFO] from plugins/ApolloLibrary/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ apollo-library --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ apollo-library --- [INFO] Changes detected - recompiling the module! :source [INFO] Compiling 17 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ apollo-library --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ apollo-library --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ apollo-library --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ apollo-library --- [INFO] Building bundle: /build/plugins/ApolloLibrary/target/apollo-library-10.0.0.jar [INFO] Writing manifest: /build/plugins/ApolloLibrary/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ apollo-library --- [INFO] Installing /build/plugins/ApolloLibrary/pom.xml to /root/.m2/repository/org/lorainelab/igb/apollo-library/10.0.0/apollo-library-10.0.0.pom [INFO] Installing /build/plugins/ApolloLibrary/target/apollo-library-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/apollo-library/10.0.0/apollo-library-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ apollo-library --- [INFO] Installing org/lorainelab/igb/apollo-library/10.0.0/apollo-library-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ apollo-library --- [INFO] Configured Artifact: org.lorainelab.igb:apollo-library:10.0.0:jar [INFO] Copying apollo-library-10.0.0.jar to /build/bundles/apollo-library-10.0.0.jar [INFO] [INFO] -------------< org.lorainelab.igb:track-operations-panel >-------------- [INFO] Building Plugin - Track Operations API, GUI 10.0.0 [26/57] [INFO] from plugins/track-operations-panel/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ track-operations-panel --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ track-operations-panel --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 8 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/track-operations-panel/src/main/java/org/lorainelab/igb/track/operations/api/OperationsPanel.java: /build/plugins/track-operations-panel/src/main/java/org/lorainelab/igb/track/operations/api/OperationsPanel.java uses unchecked or unsafe operations. [INFO] /build/plugins/track-operations-panel/src/main/java/org/lorainelab/igb/track/operations/api/OperationsPanel.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ track-operations-panel --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ track-operations-panel --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ track-operations-panel --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ track-operations-panel --- [WARNING] Bundle org.lorainelab.igb:track-operations-panel:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [WARNING] Bundle org.lorainelab.igb:track-operations-panel:bundle:10.0.0 : Export org.lorainelab.igb.track.operations.api, has 1, private references [org.lorainelab.igb.track.operations] [INFO] Building bundle: /build/plugins/track-operations-panel/target/track-operations-panel-10.0.0.jar [INFO] Writing manifest: /build/plugins/track-operations-panel/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ track-operations-panel --- [INFO] Installing /build/plugins/track-operations-panel/pom.xml to /root/.m2/repository/org/lorainelab/igb/track-operations-panel/10.0.0/track-operations-panel-10.0.0.pom [INFO] Installing /build/plugins/track-operations-panel/target/track-operations-panel-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/track-operations-panel/10.0.0/track-operations-panel-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ track-operations-panel --- [INFO] Installing org/lorainelab/igb/track-operations-panel/10.0.0/track-operations-panel-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ track-operations-panel --- [INFO] Configured Artifact: org.lorainelab.igb:track-operations-panel:10.0.0:jar [INFO] Copying track-operations-panel-10.0.0.jar to /build/bundles/track-operations-panel-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:annotation-tab >------------------ [INFO] Building Plugin - Annotation Tab 10.0.0 [27/57] [INFO] from plugins/AnnotationTab/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ annotation-tab --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ annotation-tab --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanelImpl.java: /build/plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanelImpl.java uses unchecked or unsafe operations. [INFO] /build/plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanelImpl.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ annotation-tab --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ annotation-tab --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ annotation-tab --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ annotation-tab --- [WARNING] Bundle org.lorainelab.igb:annotation-tab:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/AnnotationTab/target/annotation-tab-10.0.0.jar [INFO] Writing manifest: /build/plugins/AnnotationTab/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ annotation-tab --- [INFO] Installing /build/plugins/AnnotationTab/pom.xml to /root/.m2/repository/org/lorainelab/igb/annotation-tab/10.0.0/annotation-tab-10.0.0.pom [INFO] Installing /build/plugins/AnnotationTab/target/annotation-tab-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/annotation-tab/10.0.0/annotation-tab-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ annotation-tab --- [INFO] Installing org/lorainelab/igb/annotation-tab/10.0.0/annotation-tab-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ annotation-tab --- [INFO] Configured Artifact: org.lorainelab.igb:annotation-tab:10.0.0:jar [INFO] Copying annotation-tab-10.0.0.jar to /build/bundles/annotation-tab-10.0.0.jar [INFO] [INFO] -------------------< org.lorainelab.igb:console-tab >------------------- [INFO] Building Plugin - Console Tab 10.0.0 [28/57] [INFO] from plugins/ConsoleTab/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ console-tab --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ console-tab --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ console-tab --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ console-tab --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ console-tab --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ console-tab --- [WARNING] Bundle org.lorainelab.igb:console-tab:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/ConsoleTab/target/console-tab-10.0.0.jar [INFO] Writing manifest: /build/plugins/ConsoleTab/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ console-tab --- [INFO] Installing /build/plugins/ConsoleTab/pom.xml to /root/.m2/repository/org/lorainelab/igb/console-tab/10.0.0/console-tab-10.0.0.pom [INFO] Installing /build/plugins/ConsoleTab/target/console-tab-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/console-tab/10.0.0/console-tab-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ console-tab --- [INFO] Installing org/lorainelab/igb/console-tab/10.0.0/console-tab-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ console-tab --- [INFO] Configured Artifact: org.lorainelab.igb:console-tab:10.0.0:jar [INFO] Copying console-tab-10.0.0.jar to /build/bundles/console-tab-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:bigBedHandler >------------------ [INFO] Building Plugin - Bigbed data format handler 10.0.0 [29/57] [INFO] from plugins/BigBedHandler/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ bigBedHandler --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ bigBedHandler --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ bigBedHandler --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ bigBedHandler --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ bigBedHandler --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ bigBedHandler --- [WARNING] Bundle org.lorainelab.igb:bigBedHandler:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/BigBedHandler/target/bigBedHandler-10.0.0.jar [INFO] Writing manifest: /build/plugins/BigBedHandler/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ bigBedHandler --- [INFO] Installing /build/plugins/BigBedHandler/pom.xml to /root/.m2/repository/org/lorainelab/igb/bigBedHandler/10.0.0/bigBedHandler-10.0.0.pom [INFO] Installing /build/plugins/BigBedHandler/target/bigBedHandler-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/bigBedHandler/10.0.0/bigBedHandler-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ bigBedHandler --- [INFO] Installing org/lorainelab/igb/bigBedHandler/10.0.0/bigBedHandler-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ bigBedHandler --- [INFO] Configured Artifact: org.lorainelab.igb:bigBedHandler:10.0.0:jar [INFO] Copying bigBedHandler-10.0.0.jar to /build/bundles/bigBedHandler-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:bigWigHandler >------------------ [INFO] Building Plugin - Bigwig data format handler 10.0.0 [30/57] [INFO] from plugins/BigWigHandler/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ bigWigHandler --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ bigWigHandler --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ bigWigHandler --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ bigWigHandler --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ bigWigHandler --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ bigWigHandler --- [WARNING] Bundle org.lorainelab.igb:bigWigHandler:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/BigWigHandler/target/bigWigHandler-10.0.0.jar [INFO] Writing manifest: /build/plugins/BigWigHandler/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ bigWigHandler --- [INFO] Installing /build/plugins/BigWigHandler/pom.xml to /root/.m2/repository/org/lorainelab/igb/bigWigHandler/10.0.0/bigWigHandler-10.0.0.pom [INFO] Installing /build/plugins/BigWigHandler/target/bigWigHandler-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/bigWigHandler/10.0.0/bigWigHandler-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ bigWigHandler --- [INFO] Installing org/lorainelab/igb/bigWigHandler/10.0.0/bigWigHandler-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ bigWigHandler --- [INFO] Configured Artifact: org.lorainelab.igb:bigWigHandler:10.0.0:jar [INFO] Copying bigWigHandler-10.0.0.jar to /build/bundles/bigWigHandler-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:bookmark >--------------------- [INFO] Building Plugin - Bookmarks and REST API 10.0.0 [31/57] [INFO] from plugins/Bookmark/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ bookmark --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ bookmark --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 32 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/model/Bookmark.java: Some input files use or override a deprecated API. [INFO] /build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/model/Bookmark.java: Recompile with -Xlint:deprecation for details. [INFO] /build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkController.java: /build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkController.java uses unchecked or unsafe operations. [INFO] /build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkController.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ bookmark --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ bookmark --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ bookmark --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.affymetrix.igb.bookmarks.BookMarkTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.187 s -- in com.affymetrix.igb.bookmarks.BookMarkTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ bookmark --- [WARNING] Bundle org.lorainelab.igb:bookmark:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/Bookmark/target/bookmark-10.0.0.jar [INFO] Writing manifest: /build/plugins/Bookmark/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ bookmark --- [INFO] Installing /build/plugins/Bookmark/pom.xml to /root/.m2/repository/org/lorainelab/igb/bookmark/10.0.0/bookmark-10.0.0.pom [INFO] Installing /build/plugins/Bookmark/target/bookmark-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/bookmark/10.0.0/bookmark-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ bookmark --- [INFO] Installing org/lorainelab/igb/bookmark/10.0.0/bookmark-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ bookmark --- [INFO] Configured Artifact: org.lorainelab.igb:bookmark:10.0.0:jar [INFO] Copying bookmark-10.0.0.jar to /build/bundles/bookmark-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:externalView >------------------- [INFO] Building Plugin - External View 10.0.0 [32/57] [INFO] from plugins/ExternalView/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ externalView --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ externalView --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 12 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/ExternalView/src/main/java/com/affymetrix/igb/external/UCSCViewAction.java: Some input files use or override a deprecated API. [INFO] /build/plugins/ExternalView/src/main/java/com/affymetrix/igb/external/UCSCViewAction.java: Recompile with -Xlint:deprecation for details. [INFO] /build/plugins/ExternalView/src/main/java/com/affymetrix/igb/external/ExternalViewer.java: Some input files use unchecked or unsafe operations. [INFO] /build/plugins/ExternalView/src/main/java/com/affymetrix/igb/external/ExternalViewer.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ externalView --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ externalView --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/test-classes [INFO] /build/plugins/ExternalView/src/test/java/com/affymetrix/igb/external/EndPointTest.java: /build/plugins/ExternalView/src/test/java/com/affymetrix/igb/external/EndPointTest.java uses or overrides a deprecated API. [INFO] /build/plugins/ExternalView/src/test/java/com/affymetrix/igb/external/EndPointTest.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ externalView --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.affymetrix.igb.external.LoaderTest 15:57:48.398 INFO c.a.igb.external.ENSEMBLoader - Made URL string: {0} [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.709 s -- in com.affymetrix.igb.external.LoaderTest [INFO] Running com.affymetrix.igb.external.EndPointTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.733 s -- in com.affymetrix.igb.external.EndPointTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ externalView --- [WARNING] Bundle org.lorainelab.igb:externalView:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/ExternalView/target/externalView-10.0.0.jar [INFO] Writing manifest: /build/plugins/ExternalView/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ externalView --- [INFO] Installing /build/plugins/ExternalView/pom.xml to /root/.m2/repository/org/lorainelab/igb/externalView/10.0.0/externalView-10.0.0.pom [INFO] Installing /build/plugins/ExternalView/target/externalView-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/externalView/10.0.0/externalView-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ externalView --- [INFO] Installing org/lorainelab/igb/externalView/10.0.0/externalView-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ externalView --- [INFO] Configured Artifact: org.lorainelab.igb:externalView:10.0.0:jar [INFO] Copying externalView-10.0.0.jar to /build/bundles/externalView-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:graphTab >--------------------- [INFO] Building Plugin - Graph Tab 10.0.0 [33/57] [INFO] from plugins/GraphTab/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ graphTab --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ graphTab --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 4 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ graphTab --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ graphTab --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ graphTab --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ graphTab --- [WARNING] Bundle org.lorainelab.igb:graphTab:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/GraphTab/target/graphTab-10.0.0.jar [INFO] Writing manifest: /build/plugins/GraphTab/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ graphTab --- [INFO] Installing /build/plugins/GraphTab/pom.xml to /root/.m2/repository/org/lorainelab/igb/graphTab/10.0.0/graphTab-10.0.0.pom [INFO] Installing /build/plugins/GraphTab/target/graphTab-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/graphTab/10.0.0/graphTab-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ graphTab --- [INFO] Installing org/lorainelab/igb/graphTab/10.0.0/graphTab-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ graphTab --- [INFO] Configured Artifact: org.lorainelab.igb:graphTab:10.0.0:jar [INFO] Copying graphTab-10.0.0.jar to /build/bundles/graphTab-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:image-exporter >------------------ [INFO] Building Plugin - Save Image GUI 10.0.0 [34/57] [INFO] from plugins/image-exporter/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ image-exporter --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ image-exporter --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 9 source files with javac [debug target 21] to target/classes [WARNING] /build/plugins/image-exporter/src/main/java/org/lorainelab/igb/image/exporter/PreviewLabel.java:[30,25] Double(double) in java.lang.Double has been deprecated and marked for removal [WARNING] /build/plugins/image-exporter/src/main/java/org/lorainelab/igb/image/exporter/PreviewLabel.java:[31,26] Double(double) in java.lang.Double has been deprecated and marked for removal [INFO] /build/plugins/image-exporter/src/main/java/org/lorainelab/igb/image/exporter/ExportDialogGui.java: Some input files use unchecked or unsafe operations. [INFO] /build/plugins/image-exporter/src/main/java/org/lorainelab/igb/image/exporter/ExportDialogGui.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ image-exporter --- [INFO] skip non existing resourceDirectory /build/plugins/image-exporter/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ image-exporter --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ image-exporter --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] [INFO] Results: [INFO] [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ image-exporter --- [WARNING] Bundle org.lorainelab.igb:image-exporter:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/image-exporter/target/image-exporter-10.0.0.jar [INFO] Writing manifest: /build/plugins/image-exporter/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ image-exporter --- [INFO] Installing /build/plugins/image-exporter/pom.xml to /root/.m2/repository/org/lorainelab/igb/image-exporter/10.0.0/image-exporter-10.0.0.pom [INFO] Installing /build/plugins/image-exporter/target/image-exporter-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/image-exporter/10.0.0/image-exporter-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ image-exporter --- [INFO] Installing org/lorainelab/igb/image-exporter/10.0.0/image-exporter-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ image-exporter --- [INFO] Configured Artifact: org.lorainelab.igb:image-exporter:10.0.0:jar [INFO] Copying image-exporter-10.0.0.jar to /build/bundles/image-exporter-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:igbScript >-------------------- [INFO] Building Plugin - Script handler 10.0.0 [35/57] [INFO] from plugins/IGBScript/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ igbScript --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ igbScript --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ igbScript --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ igbScript --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ igbScript --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ igbScript --- [WARNING] Bundle org.lorainelab.igb:igbScript:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/IGBScript/target/igbScript-10.0.0.jar [INFO] Writing manifest: /build/plugins/IGBScript/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ igbScript --- [INFO] Installing /build/plugins/IGBScript/pom.xml to /root/.m2/repository/org/lorainelab/igb/igbScript/10.0.0/igbScript-10.0.0.pom [INFO] Installing /build/plugins/IGBScript/target/igbScript-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/igbScript/10.0.0/igbScript-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ igbScript --- [INFO] Installing org/lorainelab/igb/igbScript/10.0.0/igbScript-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ igbScript --- [INFO] Configured Artifact: org.lorainelab.igb:igbScript:10.0.0:jar [INFO] Copying igbScript-10.0.0.jar to /build/bundles/igbScript-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:keyWordSearch >------------------ [INFO] Building Plugin - Keyword Search 10.0.0 [36/57] [INFO] from plugins/KeyWordSearch/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ keyWordSearch --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ keyWordSearch --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ keyWordSearch --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ keyWordSearch --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ keyWordSearch --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ keyWordSearch --- [WARNING] Bundle org.lorainelab.igb:keyWordSearch:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/KeyWordSearch/target/keyWordSearch-10.0.0.jar [INFO] Writing manifest: /build/plugins/KeyWordSearch/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ keyWordSearch --- [INFO] Installing /build/plugins/KeyWordSearch/pom.xml to /root/.m2/repository/org/lorainelab/igb/keyWordSearch/10.0.0/keyWordSearch-10.0.0.pom [INFO] Installing /build/plugins/KeyWordSearch/target/keyWordSearch-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/keyWordSearch/10.0.0/keyWordSearch-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ keyWordSearch --- [INFO] Installing org/lorainelab/igb/keyWordSearch/10.0.0/keyWordSearch-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ keyWordSearch --- [INFO] Configured Artifact: org.lorainelab.igb:keyWordSearch:10.0.0:jar [INFO] Copying keyWordSearch-10.0.0.jar to /build/bundles/keyWordSearch-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:ncbiBlast >-------------------- [INFO] Building Plugin - NCBI Blast 10.0.0 [37/57] [INFO] from plugins/NCBIBlast/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ ncbiBlast --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ ncbiBlast --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 11 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/NCBIBlast/src/main/java/apollo/analysis/RemoteBlastNCBI.java: /build/plugins/NCBIBlast/src/main/java/apollo/analysis/RemoteBlastNCBI.java uses or overrides a deprecated API. [INFO] /build/plugins/NCBIBlast/src/main/java/apollo/analysis/RemoteBlastNCBI.java: Recompile with -Xlint:deprecation for details. [INFO] /build/plugins/NCBIBlast/src/main/java/apollo/analysis/RemoteBlastNCBI.java: Some input files use unchecked or unsafe operations. [INFO] /build/plugins/NCBIBlast/src/main/java/apollo/analysis/RemoteBlastNCBI.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ ncbiBlast --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ ncbiBlast --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ ncbiBlast --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running apollo.analysis.RemoteBlastNCBITest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.552 s -- in apollo.analysis.RemoteBlastNCBITest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ ncbiBlast --- [INFO] Building bundle: /build/plugins/NCBIBlast/target/ncbiBlast-10.0.0.jar [INFO] Writing manifest: /build/plugins/NCBIBlast/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ ncbiBlast --- [INFO] Installing /build/plugins/NCBIBlast/pom.xml to /root/.m2/repository/org/lorainelab/igb/ncbiBlast/10.0.0/ncbiBlast-10.0.0.pom [INFO] Installing /build/plugins/NCBIBlast/target/ncbiBlast-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/ncbiBlast/10.0.0/ncbiBlast-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ ncbiBlast --- [INFO] Installing org/lorainelab/igb/ncbiBlast/10.0.0/ncbiBlast-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ ncbiBlast --- [INFO] Configured Artifact: org.lorainelab.igb:ncbiBlast:10.0.0:jar [INFO] Copying ncbiBlast-10.0.0.jar to /build/bundles/ncbiBlast-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:propertyView >------------------- [INFO] Building Plugin - Selection Info tab 10.0.0 [38/57] [INFO] from plugins/PropertyView/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ propertyView --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ propertyView --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ propertyView --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ propertyView --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ propertyView --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ propertyView --- [WARNING] Bundle org.lorainelab.igb:propertyView:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/PropertyView/target/propertyView-10.0.0.jar [INFO] Writing manifest: /build/plugins/PropertyView/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ propertyView --- [INFO] Installing /build/plugins/PropertyView/pom.xml to /root/.m2/repository/org/lorainelab/igb/propertyView/10.0.0/propertyView-10.0.0.pom [INFO] Installing /build/plugins/PropertyView/target/propertyView-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/propertyView/10.0.0/propertyView-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ propertyView --- [INFO] Installing org/lorainelab/igb/propertyView/10.0.0/propertyView-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ propertyView --- [INFO] Configured Artifact: org.lorainelab.igb:propertyView:10.0.0:jar [INFO] Copying propertyView-10.0.0.jar to /build/bundles/propertyView-10.0.0.jar [INFO] [INFO] ----------------< org.lorainelab.igb:restrictionSites >----------------- [INFO] Building Plugin - Restriction Sites tab 10.0.0 [39/57] [INFO] from plugins/RestrictionSites/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ restrictionSites --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ restrictionSites --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/classes [INFO] /build/plugins/RestrictionSites/src/main/java/com/affymetrix/igb/restrictions/RestrictionControlView.java: /build/plugins/RestrictionSites/src/main/java/com/affymetrix/igb/restrictions/RestrictionControlView.java uses unchecked or unsafe operations. [INFO] /build/plugins/RestrictionSites/src/main/java/com/affymetrix/igb/restrictions/RestrictionControlView.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ restrictionSites --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ restrictionSites --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ restrictionSites --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ restrictionSites --- [WARNING] Bundle org.lorainelab.igb:restrictionSites:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/RestrictionSites/target/restrictionSites-10.0.0.jar [INFO] Writing manifest: /build/plugins/RestrictionSites/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ restrictionSites --- [INFO] Installing /build/plugins/RestrictionSites/pom.xml to /root/.m2/repository/org/lorainelab/igb/restrictionSites/10.0.0/restrictionSites-10.0.0.pom [INFO] Installing /build/plugins/RestrictionSites/target/restrictionSites-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/restrictionSites/10.0.0/restrictionSites-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ restrictionSites --- [INFO] Installing org/lorainelab/igb/restrictionSites/10.0.0/restrictionSites-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ restrictionSites --- [INFO] Configured Artifact: org.lorainelab.igb:restrictionSites:10.0.0:jar [INFO] Copying restrictionSites-10.0.0.jar to /build/bundles/restrictionSites-10.0.0.jar [INFO] [INFO] --------------< org.lorainelab.igb:searchModelIdOrProps >--------------- [INFO] Building Plugin - Search Id or Props 10.0.0 [40/57] [INFO] from plugins/SearchModeIdOrProps/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ searchModelIdOrProps --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ searchModelIdOrProps --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 4 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/SearchModeIdOrProps/src/main/java/com/affymetrix/igb/searchmodeidorprops/SearchModeIDOrProps.java: /build/plugins/SearchModeIdOrProps/src/main/java/com/affymetrix/igb/searchmodeidorprops/SearchModeIDOrProps.java uses or overrides a deprecated API. [INFO] /build/plugins/SearchModeIdOrProps/src/main/java/com/affymetrix/igb/searchmodeidorprops/SearchModeIDOrProps.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ searchModelIdOrProps --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ searchModelIdOrProps --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ searchModelIdOrProps --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ searchModelIdOrProps --- [WARNING] Bundle org.lorainelab.igb:searchModelIdOrProps:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/SearchModeIdOrProps/target/searchModelIdOrProps-10.0.0.jar [INFO] Writing manifest: /build/plugins/SearchModeIdOrProps/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ searchModelIdOrProps --- [INFO] Installing /build/plugins/SearchModeIdOrProps/pom.xml to /root/.m2/repository/org/lorainelab/igb/searchModelIdOrProps/10.0.0/searchModelIdOrProps-10.0.0.pom [INFO] Installing /build/plugins/SearchModeIdOrProps/target/searchModelIdOrProps-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/searchModelIdOrProps/10.0.0/searchModelIdOrProps-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ searchModelIdOrProps --- [INFO] Installing org/lorainelab/igb/searchModelIdOrProps/10.0.0/searchModelIdOrProps-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ searchModelIdOrProps --- [INFO] Configured Artifact: org.lorainelab.igb:searchModelIdOrProps:10.0.0:jar [INFO] Copying searchModelIdOrProps-10.0.0.jar to /build/bundles/searchModelIdOrProps-10.0.0.jar [INFO] [INFO] -------------------< org.lorainelab.igb:searchView >-------------------- [INFO] Building Plugin - Advanced Search Tab 10.0.0 [41/57] [INFO] from plugins/SearchView/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ searchView --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ searchView --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 5 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/SearchView/src/main/java/com/affymetrix/igb/search/SearchView.java: /build/plugins/SearchView/src/main/java/com/affymetrix/igb/search/SearchView.java uses unchecked or unsafe operations. [INFO] /build/plugins/SearchView/src/main/java/com/affymetrix/igb/search/SearchView.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ searchView --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ searchView --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ searchView --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ searchView --- [WARNING] Bundle org.lorainelab.igb:searchView:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/SearchView/target/searchView-10.0.0.jar [INFO] Writing manifest: /build/plugins/SearchView/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ searchView --- [INFO] Installing /build/plugins/SearchView/pom.xml to /root/.m2/repository/org/lorainelab/igb/searchView/10.0.0/searchView-10.0.0.pom [INFO] Installing /build/plugins/SearchView/target/searchView-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/searchView/10.0.0/searchView-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ searchView --- [INFO] Installing org/lorainelab/igb/searchView/10.0.0/searchView-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ searchView --- [INFO] Configured Artifact: org.lorainelab.igb:searchView:10.0.0:jar [INFO] Copying searchView-10.0.0.jar to /build/bundles/searchView-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:sequenceViewer >------------------ [INFO] Building Plugin - Sequence Viewer GUI 10.0.0 [42/57] [INFO] from plugins/SequenceViewer/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ sequenceViewer --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ sequenceViewer --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 11 source files with javac [debug target 1.8] to target/classes [WARNING] bootstrap class path not set in conjunction with -source 8 [WARNING] source value 8 is obsolete and will be removed in a future release [WARNING] target value 8 is obsolete and will be removed in a future release [WARNING] To suppress warnings about obsolete options, use -Xlint:-options. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ sequenceViewer --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ sequenceViewer --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ sequenceViewer --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ sequenceViewer --- [WARNING] Bundle org.lorainelab.igb:sequenceViewer:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/SequenceViewer/target/sequenceViewer-10.0.0.jar [INFO] Writing manifest: /build/plugins/SequenceViewer/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ sequenceViewer --- [INFO] Installing /build/plugins/SequenceViewer/pom.xml to /root/.m2/repository/org/lorainelab/igb/sequenceViewer/10.0.0/sequenceViewer-10.0.0.pom [INFO] Installing /build/plugins/SequenceViewer/target/sequenceViewer-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/sequenceViewer/10.0.0/sequenceViewer-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ sequenceViewer --- [INFO] Installing org/lorainelab/igb/sequenceViewer/10.0.0/sequenceViewer-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ sequenceViewer --- [INFO] Configured Artifact: org.lorainelab.igb:sequenceViewer:10.0.0:jar [INFO] Copying sequenceViewer-10.0.0.jar to /build/bundles/sequenceViewer-10.0.0.jar [INFO] [INFO] ---------------------< org.lorainelab.igb:survey >---------------------- [INFO] Building Plugin - Survey GUI 10.0.0 [43/57] [INFO] from plugins/Survey/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ survey --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ survey --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 5 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/Survey/src/main/java/com/affymetrix/igb/survey/Activator.java: /build/plugins/Survey/src/main/java/com/affymetrix/igb/survey/Activator.java uses or overrides a deprecated API. [INFO] /build/plugins/Survey/src/main/java/com/affymetrix/igb/survey/Activator.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ survey --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ survey --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ survey --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ survey --- [INFO] Building bundle: /build/plugins/Survey/target/survey-10.0.0.jar [INFO] Writing manifest: /build/plugins/Survey/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ survey --- [INFO] Installing /build/plugins/Survey/pom.xml to /root/.m2/repository/org/lorainelab/igb/survey/10.0.0/survey-10.0.0.pom [INFO] Installing /build/plugins/Survey/target/survey-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/survey/10.0.0/survey-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ survey --- [INFO] Installing org/lorainelab/igb/survey/10.0.0/survey-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ survey --- [INFO] Configured Artifact: org.lorainelab.igb:survey:10.0.0:jar [INFO] Copying survey-10.0.0.jar to /build/bundles/survey-10.0.0.jar [INFO] [INFO] ------------------< org.lorainelab.igb:thresholding >------------------- [INFO] Building Plugin - Graph thresholding visual analytics 10.0.0 [44/57] [INFO] from plugins/Thresholding/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ thresholding --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ thresholding --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 8 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/Thresholding/src/main/java/com/affymetrix/igb/thresholding/GraphScoreThreshSetter.java: /build/plugins/Thresholding/src/main/java/com/affymetrix/igb/thresholding/GraphScoreThreshSetter.java uses unchecked or unsafe operations. [INFO] /build/plugins/Thresholding/src/main/java/com/affymetrix/igb/thresholding/GraphScoreThreshSetter.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ thresholding --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ thresholding --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ thresholding --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ thresholding --- [WARNING] Bundle org.lorainelab.igb:thresholding:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/Thresholding/target/thresholding-10.0.0.jar [INFO] Writing manifest: /build/plugins/Thresholding/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ thresholding --- [INFO] Installing /build/plugins/Thresholding/pom.xml to /root/.m2/repository/org/lorainelab/igb/thresholding/10.0.0/thresholding-10.0.0.pom [INFO] Installing /build/plugins/Thresholding/target/thresholding-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/thresholding/10.0.0/thresholding-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ thresholding --- [INFO] Installing org/lorainelab/igb/thresholding/10.0.0/thresholding-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ thresholding --- [INFO] Configured Artifact: org.lorainelab.igb:thresholding:10.0.0:jar [INFO] Copying thresholding-10.0.0.jar to /build/bundles/thresholding-10.0.0.jar [INFO] [INFO] ---------------------< org.lorainelab.igb:update >---------------------- [INFO] Building Plugin - Update 10.0.0 [45/57] [INFO] from plugins/Update/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ update --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ update --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 5 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/Update/src/main/java/com/affymetrix/igb/update/Activator.java: /build/plugins/Update/src/main/java/com/affymetrix/igb/update/Activator.java uses or overrides a deprecated API. [INFO] /build/plugins/Update/src/main/java/com/affymetrix/igb/update/Activator.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ update --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ update --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ update --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ update --- [INFO] Building bundle: /build/plugins/Update/target/update-10.0.0.jar [INFO] Writing manifest: /build/plugins/Update/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ update --- [INFO] Installing /build/plugins/Update/pom.xml to /root/.m2/repository/org/lorainelab/igb/update/10.0.0/update-10.0.0.pom [INFO] Installing /build/plugins/Update/target/update-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/update/10.0.0/update-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ update --- [INFO] Installing org/lorainelab/igb/update/10.0.0/update-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ update --- [INFO] Configured Artifact: org.lorainelab.igb:update:10.0.0:jar [INFO] Copying update-10.0.0.jar to /build/bundles/update-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:plugins-manager >----------------- [INFO] Building Plugin - App Manager GUI 10.0.0 [46/57] [INFO] from plugins/plugin-manager/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' Downloading from repo1: https://maven.bioviz.org/repo1/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom Downloading from central: https://repo.maven.apache.org/maven2/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom Progress (1): 1.4 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.pom (1.4 kB at 353 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/easymock/easymock/3.4/easymock-3.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/easymock/easymock/3.4/easymock-3.4.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/easymock/easymock/3.4/easymock-3.4.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/easymock/easymock/3.4/easymock-3.4.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/easymock/easymock/3.4/easymock-3.4.pom Downloading from central: https://repo.maven.apache.org/maven2/org/easymock/easymock/3.4/easymock-3.4.pom Progress (1): 7.3 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/easymock/easymock/3.4/easymock-3.4.pom (7.3 kB at 3.7 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom Downloading from central: https://repo.maven.apache.org/maven2/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom Progress (1): 16/17 kB Progress (1): 17 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/easymock/easymock-parent/3.4/easymock-parent-3.4.pom (17 kB at 4.3 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/objenesis/objenesis/2.2/objenesis-2.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/objenesis/objenesis/2.2/objenesis-2.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/objenesis/objenesis/2.2/objenesis-2.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/objenesis/objenesis/2.2/objenesis-2.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/objenesis/objenesis/2.2/objenesis-2.2.pom Downloading from central: https://repo.maven.apache.org/maven2/org/objenesis/objenesis/2.2/objenesis-2.2.pom Progress (1): 2.5 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/objenesis/objenesis/2.2/objenesis-2.2.pom (2.5 kB at 826 kB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom Downloading from repo2: https://maven.bioviz.org/repo2/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom Downloading from repo3: https://maven.bioviz.org/repo3/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom Downloading from central: https://repo.maven.apache.org/maven2/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom Progress (1): 16/17 kB Progress (1): 17 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/objenesis/objenesis-parent/2.2/objenesis-parent-2.2.pom (17 kB at 4.1 MB/s) Downloading from repo1: https://maven.bioviz.org/repo1/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar Downloading from repo1: https://maven.bioviz.org/repo1/org/easymock/easymock/3.4/easymock-3.4.jar Downloading from repo1: https://maven.bioviz.org/repo1/org/objenesis/objenesis/2.2/objenesis-2.2.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/easymock/easymock/3.4/easymock-3.4.jar Downloading from repo2: https://maven.bioviz.org/repo2/org/objenesis/objenesis/2.2/objenesis-2.2.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/easymock/easymock/3.4/easymock-3.4.jar Downloading from repo3: https://maven.bioviz.org/repo3/org/objenesis/objenesis/2.2/objenesis-2.2.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/easymock/easymock/3.4/easymock-3.4.jar Downloading from maven-releases: https://nexus.bioviz.org/repository/maven-releases/org/objenesis/objenesis/2.2/objenesis-2.2.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/easymock/easymock/3.4/easymock-3.4.jar Downloading from igb-dev: https://nexus.bioviz.org/repository/igb-dev/org/objenesis/objenesis/2.2/objenesis-2.2.jar Downloading from central: https://repo.maven.apache.org/maven2/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar Progress (1): 16/430 kB Progress (1): 33/430 kB Progress (1): 49/430 kB Progress (1): 66/430 kB Progress (1): 82/430 kB Progress (1): 98/430 kB Progress (1): 115/430 kB Progress (1): 131/430 kB Progress (1): 147/430 kB Progress (1): 164/430 kB Progress (1): 180/430 kB Progress (1): 197/430 kB Progress (1): 213/430 kB Progress (1): 229/430 kB Progress (1): 246/430 kB Progress (1): 262/430 kB Progress (1): 279/430 kB Progress (1): 295/430 kB Progress (1): 311/430 kB Progress (1): 328/430 kB Progress (1): 344/430 kB Progress (1): 360/430 kB Progress (1): 377/430 kB Progress (1): 393/430 kB Progress (1): 410/430 kB Progress (1): 426/430 kB Progress (1): 430 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/osgi/org.osgi.core/5.0.0/org.osgi.core-5.0.0.jar (430 kB at 20 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/easymock/easymock/3.4/easymock-3.4.jar Downloading from central: https://repo.maven.apache.org/maven2/org/objenesis/objenesis/2.2/objenesis-2.2.jar Progress (1): 16/474 kB Progress (1): 33/474 kB Progress (1): 49/474 kB Progress (1): 66/474 kB Progress (1): 82/474 kB Progress (1): 98/474 kB Progress (1): 115/474 kB Progress (2): 115/474 kB | 16/53 kB Progress (2): 115/474 kB | 33/53 kB Progress (2): 115/474 kB | 49/53 kB Progress (2): 115/474 kB | 53 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/objenesis/objenesis/2.2/objenesis-2.2.jar (53 kB at 3.5 MB/s) Progress (1): 131/474 kB Progress (1): 147/474 kB Progress (1): 164/474 kB Progress (1): 180/474 kB Progress (1): 197/474 kB Progress (1): 213/474 kB Progress (1): 229/474 kB Progress (1): 246/474 kB Progress (1): 256/474 kB Progress (1): 272/474 kB Progress (1): 289/474 kB Progress (1): 305/474 kB Progress (1): 321/474 kB Progress (1): 338/474 kB Progress (1): 354/474 kB Progress (1): 370/474 kB Progress (1): 387/474 kB Progress (1): 403/474 kB Progress (1): 420/474 kB Progress (1): 436/474 kB Progress (1): 452/474 kB Progress (1): 469/474 kB Progress (1): 474 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/easymock/easymock/3.4/easymock-3.4.jar (474 kB at 19 MB/s) [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ plugins-manager --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 32 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ plugins-manager --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 24 source files with javac [debug target 21] to target/classes [WARNING] unknown enum constant jakarta.xml.bind.annotation.XmlAccessType.FIELD reason: class file for jakarta.xml.bind.annotation.XmlAccessType not found [WARNING] unknown enum constant jakarta.xml.bind.annotation.XmlAccessType.FIELD [INFO] /build/plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/repos/PluginRepositoryList.java: Some input files use or override a deprecated API. [INFO] /build/plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/repos/PluginRepositoryList.java: Recompile with -Xlint:deprecation for details. [INFO] /build/plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/AppManagerFxPanel.java: /build/plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/AppManagerFxPanel.java uses unchecked or unsafe operations. [INFO] /build/plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/AppManagerFxPanel.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ plugins-manager --- [INFO] Copying 2 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ plugins-manager --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ plugins-manager --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.plugin.manager.PluginManagerFxPanelTest [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.084 s -- in org.lorainelab.igb.plugin.manager.PluginManagerFxPanelTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ plugins-manager --- [WARNING] Bundle org.lorainelab.igb:plugins-manager:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/plugin-manager/target/plugins-manager-10.0.0.jar [INFO] Writing manifest: /build/plugins/plugin-manager/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ plugins-manager --- [INFO] Installing /build/plugins/plugin-manager/pom.xml to /root/.m2/repository/org/lorainelab/igb/plugins-manager/10.0.0/plugins-manager-10.0.0.pom [INFO] Installing /build/plugins/plugin-manager/target/plugins-manager-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/plugins-manager/10.0.0/plugins-manager-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ plugins-manager --- [INFO] Installing org/lorainelab/igb/plugins-manager/10.0.0/plugins-manager-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ plugins-manager --- [INFO] Configured Artifact: org.lorainelab.igb:plugins-manager:10.0.0:jar [INFO] Copying plugins-manager-10.0.0.jar to /build/bundles/plugins-manager-10.0.0.jar [INFO] [INFO] ------------< org.lorainelab.igb:paired-data-preprocessor >------------- [INFO] Building Plugin - Paired-end Read Preprocessor 10.0.0 [47/57] [INFO] from plugins/PairedEndDataPreprocessor/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ paired-data-preprocessor --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/PairedEndDataPreprocessor/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ paired-data-preprocessor --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ paired-data-preprocessor --- [INFO] skip non existing resourceDirectory /build/plugins/PairedEndDataPreprocessor/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ paired-data-preprocessor --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ paired-data-preprocessor --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ paired-data-preprocessor --- [WARNING] Bundle org.lorainelab.igb:paired-data-preprocessor:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/PairedEndDataPreprocessor/target/paired-data-preprocessor-10.0.0.jar [INFO] Writing manifest: /build/plugins/PairedEndDataPreprocessor/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ paired-data-preprocessor --- [INFO] Installing /build/plugins/PairedEndDataPreprocessor/pom.xml to /root/.m2/repository/org/lorainelab/igb/paired-data-preprocessor/10.0.0/paired-data-preprocessor-10.0.0.pom [INFO] Installing /build/plugins/PairedEndDataPreprocessor/target/paired-data-preprocessor-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/paired-data-preprocessor/10.0.0/paired-data-preprocessor-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ paired-data-preprocessor --- [INFO] Installing org/lorainelab/igb/paired-data-preprocessor/10.0.0/paired-data-preprocessor-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ paired-data-preprocessor --- [INFO] Configured Artifact: org.lorainelab.igb:paired-data-preprocessor:10.0.0:jar [INFO] Copying paired-data-preprocessor-10.0.0.jar to /build/bundles/dynamic/paired-data-preprocessor-10.0.0.jar [INFO] [INFO] -----------------< org.lorainelab.igb:session-manager >----------------- [INFO] Building Plugin - Save Session Manager 10.0.0 [48/57] [INFO] from plugins/session-manager/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ session-manager --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 3 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ session-manager --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ session-manager --- [INFO] skip non existing resourceDirectory /build/plugins/session-manager/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ session-manager --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ session-manager --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ session-manager --- [WARNING] Bundle org.lorainelab.igb:session-manager:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/session-manager/target/session-manager-10.0.0.jar [INFO] Writing manifest: /build/plugins/session-manager/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ session-manager --- [INFO] Installing /build/plugins/session-manager/pom.xml to /root/.m2/repository/org/lorainelab/igb/session-manager/10.0.0/session-manager-10.0.0.pom [INFO] Installing /build/plugins/session-manager/target/session-manager-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/session-manager/10.0.0/session-manager-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ session-manager --- [INFO] Installing org/lorainelab/igb/session-manager/10.0.0/session-manager-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ session-manager --- [INFO] Configured Artifact: org.lorainelab.igb:session-manager:10.0.0:jar [INFO] Copying session-manager-10.0.0.jar to /build/bundles/session-manager-10.0.0.jar [INFO] [INFO] ---------------< org.lorainelab.igb:keybinding-registry >--------------- [INFO] Building Plugin - Toolbar Preferences GUI 10.0.0 [49/57] [INFO] from plugins/Keybinding-registry/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ keybinding-registry --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ keybinding-registry --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/Keybinding-registry/src/main/java/org/lorainelab/igb/keystrokes/KeyStrokesView.java: Some input files use or override a deprecated API. [INFO] /build/plugins/Keybinding-registry/src/main/java/org/lorainelab/igb/keystrokes/KeyStrokesView.java: Recompile with -Xlint:deprecation for details. [INFO] /build/plugins/Keybinding-registry/src/main/java/org/lorainelab/igb/keystrokes/model/KeyStrokeViewTableModel.java: /build/plugins/Keybinding-registry/src/main/java/org/lorainelab/igb/keystrokes/model/KeyStrokeViewTableModel.java uses unchecked or unsafe operations. [INFO] /build/plugins/Keybinding-registry/src/main/java/org/lorainelab/igb/keystrokes/model/KeyStrokeViewTableModel.java: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ keybinding-registry --- [INFO] skip non existing resourceDirectory /build/plugins/Keybinding-registry/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ keybinding-registry --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ keybinding-registry --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ keybinding-registry --- [WARNING] Bundle org.lorainelab.igb:keybinding-registry:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/Keybinding-registry/target/keybinding-registry-10.0.0.jar [INFO] Writing manifest: /build/plugins/Keybinding-registry/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ keybinding-registry --- [INFO] Installing /build/plugins/Keybinding-registry/pom.xml to /root/.m2/repository/org/lorainelab/igb/keybinding-registry/10.0.0/keybinding-registry-10.0.0.pom [INFO] Installing /build/plugins/Keybinding-registry/target/keybinding-registry-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/keybinding-registry/10.0.0/keybinding-registry-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ keybinding-registry --- [INFO] Installing org/lorainelab/igb/keybinding-registry/10.0.0/keybinding-registry-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ keybinding-registry --- [INFO] Configured Artifact: org.lorainelab.igb:keybinding-registry:10.0.0:jar [INFO] Copying keybinding-registry-10.0.0.jar to /build/bundles/keybinding-registry-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:feedback >--------------------- [INFO] Building Plugin - Feedback 10.0.0 [50/57] [INFO] from plugins/feedback/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ feedback --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 5 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ feedback --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ feedback --- [INFO] skip non existing resourceDirectory /build/plugins/feedback/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ feedback --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ feedback --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ feedback --- [WARNING] Bundle org.lorainelab.igb:feedback:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/feedback/target/feedback-10.0.0.jar [INFO] Writing manifest: /build/plugins/feedback/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ feedback --- [INFO] Installing /build/plugins/feedback/pom.xml to /root/.m2/repository/org/lorainelab/igb/feedback/10.0.0/feedback-10.0.0.pom [INFO] Installing /build/plugins/feedback/target/feedback-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/feedback/10.0.0/feedback-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ feedback --- [INFO] Installing org/lorainelab/igb/feedback/10.0.0/feedback-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ feedback --- [INFO] Configured Artifact: org.lorainelab.igb:feedback:10.0.0:jar [INFO] Copying feedback-10.0.0.jar to /build/bundles/dynamic/feedback-10.0.0.jar [INFO] [INFO] -------------------< org.lorainelab.igb:narrowpeak >-------------------- [INFO] Building Plugin - Narrowpeak data format handler 10.0.0 [51/57] [INFO] from plugins/narrowpeak/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ narrowpeak --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/narrowpeak/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ narrowpeak --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ narrowpeak --- [INFO] Copying 1 resource from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ narrowpeak --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ narrowpeak --- [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ narrowpeak --- [WARNING] Bundle org.lorainelab.igb:narrowpeak:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/narrowpeak/target/narrowpeak-10.0.0.jar [INFO] Writing manifest: /build/plugins/narrowpeak/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ narrowpeak --- [INFO] Installing /build/plugins/narrowpeak/pom.xml to /root/.m2/repository/org/lorainelab/igb/narrowpeak/10.0.0/narrowpeak-10.0.0.pom [INFO] Installing /build/plugins/narrowpeak/target/narrowpeak-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/narrowpeak/10.0.0/narrowpeak-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ narrowpeak --- [INFO] Installing org/lorainelab/igb/narrowpeak/10.0.0/narrowpeak-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ narrowpeak --- [INFO] Configured Artifact: org.lorainelab.igb:narrowpeak:10.0.0:jar [INFO] Copying narrowpeak-10.0.0.jar to /build/bundles/dynamic/narrowpeak-10.0.0.jar [INFO] [INFO] -------------------< org.lorainelab.igb:genotyping >-------------------- [INFO] Building Plugin - File Handler - Genotyping Results 10.0.0 [52/57] [INFO] from plugins/GenotypingResults/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ genotyping --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/GenotypingResults/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ genotyping --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 5 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/GenotypingResults/src/main/java/org/lorainelab/igb/genotyping/GenotypingResultsFactory.java: /build/plugins/GenotypingResults/src/main/java/org/lorainelab/igb/genotyping/GenotypingResultsFactory.java uses or overrides a deprecated API. [INFO] /build/plugins/GenotypingResults/src/main/java/org/lorainelab/igb/genotyping/GenotypingResultsFactory.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ genotyping --- [INFO] Copying 2 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ genotyping --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ genotyping --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.639 s -- in org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ genotyping --- [WARNING] Bundle org.lorainelab.igb:genotyping:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/GenotypingResults/target/genotyping-10.0.0.jar [INFO] Writing manifest: /build/plugins/GenotypingResults/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ genotyping --- [INFO] Installing /build/plugins/GenotypingResults/pom.xml to /root/.m2/repository/org/lorainelab/igb/genotyping/10.0.0/genotyping-10.0.0.pom [INFO] Installing /build/plugins/GenotypingResults/target/genotyping-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/genotyping/10.0.0/genotyping-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ genotyping --- [INFO] Installing org/lorainelab/igb/genotyping/10.0.0/genotyping-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ genotyping --- [INFO] Configured Artifact: org.lorainelab.igb:genotyping:10.0.0:jar [INFO] Copying genotyping-10.0.0.jar to /build/bundles/dynamic/genotyping-10.0.0.jar [INFO] [INFO] -----------------------< org.lorainelab.igb:bed >----------------------- [INFO] Building Plugin - BED file format handler 10.0.0 [53/57] [INFO] from plugins/bed/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ bed --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/bed/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ bed --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ bed --- [INFO] Copying 4 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ bed --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 1 source file with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ bed --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.bed.BedParserTest 15:58:12.397 [main] DEBUG com.google.code.externalsorting.ExternalMergeSort - Temp file count: 1 15:58:12.533 [main] DEBUG com.google.code.externalsorting.ExternalMergeSort - Temp file count: 1 15:58:12.634 [main] DEBUG com.google.code.externalsorting.ExternalMergeSort - Temp file count: 1 15:58:12.707 [main] DEBUG com.google.code.externalsorting.ExternalMergeSort - Temp file count: 1 15:58:12.780 [main] DEBUG com.google.code.externalsorting.ExternalMergeSort - Temp file count: 1 [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.085 s -- in org.lorainelab.igb.bed.BedParserTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ bed --- [WARNING] Bundle org.lorainelab.igb:bed:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/bed/target/bed-10.0.0.jar [INFO] Writing manifest: /build/plugins/bed/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ bed --- [INFO] Installing /build/plugins/bed/pom.xml to /root/.m2/repository/org/lorainelab/igb/bed/10.0.0/bed-10.0.0.pom [INFO] Installing /build/plugins/bed/target/bed-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/bed/10.0.0/bed-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ bed --- [INFO] Installing org/lorainelab/igb/bed/10.0.0/bed-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ bed --- [INFO] Configured Artifact: org.lorainelab.igb:bed:10.0.0:jar [INFO] Copying bed-10.0.0.jar to /build/bundles/dynamic/bed-10.0.0.jar [INFO] [INFO] -----------------------< org.lorainelab.igb:bam >----------------------- [INFO] Building Plugin - BAM data format handler 10.0.0 [54/57] [INFO] from plugins/bam/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ bam --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/bam/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ bam --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 5 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/bam/src/main/java/org/lorainelab/igb/bam/SAM.java: Some input files use or override a deprecated API. [INFO] /build/plugins/bam/src/main/java/org/lorainelab/igb/bam/SAM.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ bam --- [INFO] Copying 3 resources from src/test/resources to target/test-classes [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ bam --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/test-classes [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ bam --- [INFO] Using auto detected provider org.apache.maven.surefire.junitplatform.JUnitPlatformProvider [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.bam.SAMParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.675 s -- in org.lorainelab.igb.bam.SAMParserTest [INFO] Running org.lorainelab.igb.bam.BAMParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.264 s -- in org.lorainelab.igb.bam.BAMParserTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ bam --- [WARNING] Bundle org.lorainelab.igb:bam:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/bam/target/bam-10.0.0.jar [INFO] Writing manifest: /build/plugins/bam/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ bam --- [INFO] Installing /build/plugins/bam/pom.xml to /root/.m2/repository/org/lorainelab/igb/bam/10.0.0/bam-10.0.0.pom [INFO] Installing /build/plugins/bam/target/bam-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/bam/10.0.0/bam-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ bam --- [INFO] Installing org/lorainelab/igb/bam/10.0.0/bam-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ bam --- [INFO] Configured Artifact: org.lorainelab.igb:bam:10.0.0:jar [INFO] Copying bam-10.0.0.jar to /build/bundles/dynamic/bam-10.0.0.jar [INFO] [INFO] -----------------------< org.lorainelab.igb:bai >----------------------- [INFO] Building Plugin - BAI index visualization handler 10.0.0 [55/57] [INFO] from plugins/bai/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ bai --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] Copying 1 resource from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ bai --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ bai --- [INFO] skip non existing resourceDirectory /build/plugins/bai/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ bai --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ bai --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ bai --- [WARNING] Bundle org.lorainelab.igb:bai:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/bai/target/bai-10.0.0.jar [INFO] Writing manifest: /build/plugins/bai/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ bai --- [INFO] Installing /build/plugins/bai/pom.xml to /root/.m2/repository/org/lorainelab/igb/bai/10.0.0/bai-10.0.0.pom [INFO] Installing /build/plugins/bai/target/bai-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/bai/10.0.0/bai-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ bai --- [INFO] Installing org/lorainelab/igb/bai/10.0.0/bai-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ bai --- [INFO] Configured Artifact: org.lorainelab.igb:bai:10.0.0:jar [INFO] Copying bai-10.0.0.jar to /build/bundles/dynamic/bai-10.0.0.jar [INFO] [INFO] --------------------< org.lorainelab.igb:appstore >--------------------- [INFO] Building Plugin - App Store REST API 10.0.0 [56/57] [INFO] from plugins/AppStore/pom.xml [INFO] -------------------------------[ bundle ]------------------------------- [WARNING] Parameter 'ignoreChecksumFailure' is unknown for plugin 'maven-dependency-plugin:3.5.0:copy (copy)' [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ appstore --- [INFO] Copying 0 resource from src/main/java to target/classes [INFO] skip non existing resourceDirectory /build/plugins/AppStore/src/main/resources [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ appstore --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 2 source files with javac [debug target 21] to target/classes [INFO] /build/plugins/AppStore/src/main/java/org/lorainelab/igb/appstore/IgbAppServer.java: /build/plugins/AppStore/src/main/java/org/lorainelab/igb/appstore/IgbAppServer.java uses or overrides a deprecated API. [INFO] /build/plugins/AppStore/src/main/java/org/lorainelab/igb/appstore/IgbAppServer.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ appstore --- [INFO] skip non existing resourceDirectory /build/plugins/AppStore/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ appstore --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ appstore --- [INFO] No tests to run. [INFO] [INFO] --- bundle:5.1.9:bundle (default-bundle) @ appstore --- [WARNING] Bundle org.lorainelab.igb:appstore:bundle:10.0.0 : Service-Component is normally generated by bnd. If you want to point at specific component XML files (wildcards are allowed, see findEntries) make sure it ends in '.xml'. Found * [INFO] Building bundle: /build/plugins/AppStore/target/appstore-10.0.0.jar [INFO] Writing manifest: /build/plugins/AppStore/target/classes/META-INF/MANIFEST.MF [INFO] [INFO] --- install:3.1.1:install (default-install) @ appstore --- [INFO] Installing /build/plugins/AppStore/pom.xml to /root/.m2/repository/org/lorainelab/igb/appstore/10.0.0/appstore-10.0.0.pom [INFO] Installing /build/plugins/AppStore/target/appstore-10.0.0.jar to /root/.m2/repository/org/lorainelab/igb/appstore/10.0.0/appstore-10.0.0.jar [INFO] [INFO] --- bundle:5.1.9:install (default-install) @ appstore --- [INFO] Installing org/lorainelab/igb/appstore/10.0.0/appstore-10.0.0.jar [INFO] Writing OBR metadata [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ appstore --- [INFO] Configured Artifact: org.lorainelab.igb:appstore:10.0.0:jar [INFO] Copying appstore-10.0.0.jar to /build/bundles/appstore-10.0.0.jar [INFO] [INFO] ----------------------< org.lorainelab.igb:main >----------------------- [INFO] Building IGB Main (run me) 10.0.0 [57/57] [INFO] from main/pom.xml [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/3.0.0/exec-maven-plugin-3.0.0.pom Progress (1): 14 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/3.0.0/exec-maven-plugin-3.0.0.pom (14 kB at 2.7 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/mojo-parent/50/mojo-parent-50.pom Progress (1): 16/34 kB Progress (1): 32/34 kB Progress (1): 34 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/mojo-parent/50/mojo-parent-50.pom (34 kB at 11 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/3.0.0/exec-maven-plugin-3.0.0.jar Progress (1): 16/68 kB Progress (1): 32/68 kB Progress (1): 49/68 kB Progress (1): 65/68 kB Progress (1): 68 kB 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target/classes [INFO] Copying 2 resources from src/main/resources to target/classes [INFO] [INFO] --- compiler:3.11.0:compile (default-compile) @ main --- [INFO] Changes detected - recompiling the module! :dependency [INFO] Compiling 3 source files with javac [debug target 21] to target/classes [INFO] /build/main/src/main/java/com/affymetrix/main/DefaultURLStreamHandlerFactory.java: /build/main/src/main/java/com/affymetrix/main/DefaultURLStreamHandlerFactory.java uses or overrides a deprecated API. [INFO] /build/main/src/main/java/com/affymetrix/main/DefaultURLStreamHandlerFactory.java: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ main --- [INFO] skip non existing resourceDirectory /build/main/src/test/resources [INFO] [INFO] --- compiler:3.11.0:testCompile (default-testCompile) @ main --- [INFO] No sources to compile [INFO] [INFO] --- surefire:3.1.2:test (default-test) @ main --- [INFO] No tests to run. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ main --- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.1.0/file-management-3.1.0.pom Progress (1): 4.5 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.1.0/file-management-3.1.0.pom (4.5 kB at 1.5 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/36/maven-shared-components-36.pom Progress (1): 4.9 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/36/maven-shared-components-36.pom (4.9 kB at 2.4 MB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/36/maven-parent-36.pom Progress (1): 16/45 kB Progress (1): 33/45 kB Progress (1): 45 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/36/maven-parent-36.pom (45 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/build/main/target/lib/jakarta.activation-api-2.1.2.jar [INFO] Copying jaxb-core-4.0.1.jar to /build/main/target/lib/jaxb-core-4.0.1.jar [INFO] Copying txw2-4.0.4.jar to /build/main/target/lib/txw2-4.0.4.jar [INFO] Copying istack-commons-runtime-4.2.0.jar to /build/main/target/lib/istack-commons-runtime-4.2.0.jar [INFO] Copying FastInfoset-2.1.1.jar to /build/main/target/lib/FastInfoset-2.1.1.jar [INFO] Copying osgi-resource-locator-2.5.0-b42.jar to /build/main/target/lib/osgi-resource-locator-2.5.0-b42.jar [INFO] Copying affymetrix-common-10.0.0.jar to /build/main/target/lib/affymetrix-common-10.0.0.jar [INFO] Copying igb-10.0.0.jar to /build/main/target/lib/igb-10.0.0.jar [INFO] Copying igb-services-10.0.0.jar to /build/main/target/lib/igb-services-10.0.0.jar [INFO] Copying shared-lib-wrapper-10.0.0.jar to /build/main/target/lib/shared-lib-wrapper-10.0.0.jar [INFO] Copying org.apache.felix.main-7.0.5.jar to /build/main/target/lib/org.apache.felix.main-7.0.5.jar [INFO] Copying heatmap-editor-10.0.0.jar to /build/main/target/lib/heatmap-editor-10.0.0.jar [INFO] Copying genometry-10.0.0.jar to /build/main/target/lib/genometry-10.0.0.jar [INFO] Copying igbSwingExt-10.0.0.jar to /build/main/target/lib/igbSwingExt-10.0.0.jar [INFO] Copying window-service-10.0.0.jar to /build/main/target/lib/window-service-10.0.0.jar [INFO] Copying session-manager-10.0.0.jar to /build/main/target/lib/session-manager-10.0.0.jar [INFO] Copying keybinding-registry-10.0.0.jar to /build/main/target/lib/keybinding-registry-10.0.0.jar [INFO] Copying igb-preferences-10.0.0.jar to /build/main/target/lib/igb-preferences-10.0.0.jar [INFO] Copying weblinks-10.0.0.jar to /build/main/target/lib/weblinks-10.0.0.jar [INFO] Copying synonym-lookup-10.0.0.jar to /build/main/target/lib/synonym-lookup-10.0.0.jar [INFO] Copying quickload-10.0.0.jar to /build/main/target/lib/quickload-10.0.0.jar [INFO] Copying das-10.0.0.jar to /build/main/target/lib/das-10.0.0.jar [INFO] Copying frameManager-10.0.0.jar to /build/main/target/lib/frameManager-10.0.0.jar [INFO] Copying igb-javafx-util-10.0.0.jar to /build/main/target/lib/igb-javafx-util-10.0.0.jar [INFO] Copying guava-32.1.1-jre.jar to /build/main/target/lib/guava-32.1.1-jre.jar [INFO] Copying failureaccess-1.0.1.jar to /build/main/target/lib/failureaccess-1.0.1.jar [INFO] Copying gson-2.10.1.jar to /build/main/target/lib/gson-2.10.1.jar [INFO] Copying commons-lang3-3.12.0.jar to /build/main/target/lib/commons-lang3-3.12.0.jar [INFO] Copying commons-csv-1.10.0.jar to /build/main/target/lib/commons-csv-1.10.0.jar [INFO] Copying commons-io-2.11.0.jar to /build/main/target/lib/commons-io-2.11.0.jar [INFO] Copying genoviz-1.1.9.jar to /build/main/target/lib/genoviz-1.1.9.jar [INFO] Copying bigwig-2.0.1.jar to /build/main/target/lib/bigwig-2.0.1.jar [INFO] Copying commons-compress-1.23.0.jar to /build/main/target/lib/commons-compress-1.23.0.jar [INFO] Copying commons-logging-1.2.jar to /build/main/target/lib/commons-logging-1.2.jar [INFO] 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[INFO] Copying flatlaf-jide-oss-3.2.5.jar to /build/main/target/lib/flatlaf-jide-oss-3.2.5.jar [INFO] Copying logback-core-1.2.12.jar to /build/main/target/lib/logback-core-1.2.12.jar [INFO] Copying logback-classic-1.2.12.jar to /build/main/target/lib/logback-classic-1.2.12.jar [INFO] Copying logging-config-10.0.0.jar to /build/main/target/lib/logging-config-10.0.0.jar [INFO] Copying igb-genoviz-extensions-10.0.0.jar to /build/main/target/lib/igb-genoviz-extensions-10.0.0.jar [INFO] Copying org.apache.felix.scr-2.2.6.jar to /build/main/target/lib/org.apache.felix.scr-2.2.6.jar [INFO] Copying org.osgi.service.component-1.5.1.jar to /build/main/target/lib/org.osgi.service.component-1.5.1.jar [INFO] Copying org.osgi.util.promise-1.3.0.jar to /build/main/target/lib/org.osgi.util.promise-1.3.0.jar [INFO] Copying org.osgi.util.function-1.2.0.jar to /build/main/target/lib/org.osgi.util.function-1.2.0.jar [INFO] Copying external-sort-10.0.0.jar to /build/main/target/lib/external-sort-10.0.0.jar [INFO] Copying org.lorainelab.igb.menu.api-10.0.0.jar to /build/main/target/lib/org.lorainelab.igb.menu.api-10.0.0.jar [INFO] Copying context-menu-service-10.0.0.jar to /build/main/target/lib/context-menu-service-10.0.0.jar [INFO] Copying track-operations-panel-10.0.0.jar to /build/main/target/lib/track-operations-panel-10.0.0.jar [INFO] Copying org.apache.felix.configadmin-1.9.26.jar to /build/main/target/lib/org.apache.felix.configadmin-1.9.26.jar [INFO] Copying org.apache.felix.http.servlet-api-2.1.0.jar to /build/main/target/lib/org.apache.felix.http.servlet-api-2.1.0.jar [INFO] Copying org.apache.felix.http.jetty-5.1.4.jar to /build/main/target/lib/org.apache.felix.http.jetty-5.1.4.jar [INFO] Copying org.apache.felix.http.base-5.1.2.jar to /build/main/target/lib/org.apache.felix.http.base-5.1.2.jar [INFO] [INFO] --- dependency:3.5.0:copy (copy) @ main --- [INFO] Configured Artifact: org.lorainelab.igb:main:10.0.0:jar [INFO] Copying 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1.9/1.9 MB Progress (1): 1.9/1.9 MB Progress (1): 1.9/1.9 MB Progress (1): 1.9/1.9 MB Progress (1): 1.9 MB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/ant/ant/1.8.2/ant-1.8.2.jar (1.9 MB at 23 MB/s) [INFO] Executing tasks main: [jar] Building jar: /build/igb_exe.jar [INFO] Executed tasks [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for IGB Project 10.0.0: [INFO] [INFO] IGB Project ........................................ SUCCESS [ 0.478 s] [INFO] Flatlaf - Look and feel configuration .............. SUCCESS [ 15.200 s] [INFO] Core - Heatmap Editor .............................. SUCCESS [ 4.620 s] [INFO] Core - Affymetrix Common ........................... SUCCESS [ 3.412 s] [INFO] Plugin - Sorting API and Impl ...................... SUCCESS [ 4.984 s] [INFO] Plugin - Data caching API .......................... SUCCESS [ 0.380 s] [INFO] Core - Synonym Lookup .............................. SUCCESS [ 3.059 s] [INFO] Core - Genometry (Data Models) ..................... SUCCESS [ 22.024 s] [INFO] Core - Preferences ................................. SUCCESS [ 3.361 s] [INFO] Core - IGB Swing Extensions ........................ SUCCESS [ 1.542 s] [INFO] Core - Genoviz Extensions .......................... SUCCESS [ 0.570 s] [INFO] Core - IGB Services API ............................ SUCCESS [ 0.689 s] [INFO] Core - Frame Manager ............................... SUCCESS [ 0.785 s] [INFO] Core - Window Service .............................. SUCCESS [ 0.675 s] [INFO] Core - JavaFX Utilities ............................ SUCCESS [ 0.346 s] [INFO] Core - Menu API .................................... SUCCESS [ 0.418 s] [INFO] Core - Context Menu Service ........................ SUCCESS [ 0.332 s] [INFO] Core - IGB ......................................... SUCCESS [ 15.977 s] [INFO] Core - Bundle wrapper, deployer .................... SUCCESS [ 7.681 s] [INFO] Core - Logging Config .............................. SUCCESS [ 0.190 s] [INFO] Core - Web Links ................................... SUCCESS [ 0.941 s] [INFO] Plugin - Data caching GUI .......................... SUCCESS [ 2.787 s] [INFO] Core - Quickload (data source) ..................... SUCCESS [ 3.167 s] [INFO] Core - DAS (data source) ........................... SUCCESS [ 6.341 s] [INFO] Plugin - Apollo Library ............................ SUCCESS [ 0.381 s] [INFO] Plugin - Track Operations API, GUI ................. SUCCESS [ 0.492 s] [INFO] Plugin - Annotation Tab ............................ SUCCESS [ 0.628 s] [INFO] Plugin - Console Tab ............................... SUCCESS [ 0.414 s] [INFO] Plugin - Bigbed data format handler ................ SUCCESS [ 0.356 s] [INFO] Plugin - Bigwig data format handler ................ SUCCESS [ 0.372 s] [INFO] Plugin - Bookmarks and REST API .................... SUCCESS [ 2.894 s] [INFO] Plugin - External View ............................. SUCCESS [ 7.476 s] [INFO] Plugin - Graph Tab ................................. SUCCESS [ 0.480 s] [INFO] Plugin - Save Image GUI ............................ SUCCESS [ 2.168 s] [INFO] Plugin - Script handler ............................ SUCCESS [ 0.480 s] [INFO] Plugin - Keyword Search ............................ SUCCESS [ 0.343 s] [INFO] Plugin - NCBI Blast ................................ SUCCESS [ 3.496 s] [INFO] Plugin - Selection Info tab ........................ SUCCESS [ 0.626 s] [INFO] Plugin - Restriction Sites tab ..................... SUCCESS [ 0.343 s] [INFO] Plugin - Search Id or Props ........................ SUCCESS [ 0.342 s] [INFO] Plugin - Advanced Search Tab ....................... SUCCESS [ 0.703 s] [INFO] Plugin - Sequence Viewer GUI ....................... SUCCESS [ 0.871 s] [INFO] Plugin - Survey GUI ................................ SUCCESS [ 0.485 s] [INFO] Plugin - Graph thresholding visual analytics ....... SUCCESS [ 0.594 s] [INFO] Plugin - Update .................................... SUCCESS [ 0.395 s] [INFO] Plugin - App Manager GUI ........................... SUCCESS [ 3.962 s] [INFO] Plugin - Paired-end Read Preprocessor .............. SUCCESS [ 0.385 s] [INFO] Plugin - Save Session Manager ...................... SUCCESS [ 0.432 s] [INFO] Plugin - Toolbar Preferences GUI ................... SUCCESS [ 0.877 s] [INFO] Plugin - Feedback .................................. SUCCESS [ 0.471 s] [INFO] Plugin - Narrowpeak data format handler ............ SUCCESS [ 0.375 s] [INFO] Plugin - File Handler - Genotyping Results ........ SUCCESS [ 2.461 s] [INFO] Plugin - BED file format handler ................... SUCCESS [ 3.290 s] [INFO] Plugin - BAM data format handler ................... SUCCESS [ 2.702 s] [INFO] Plugin - BAI index visualization handler ........... SUCCESS [ 0.497 s] [INFO] Plugin - App Store REST API ........................ SUCCESS [ 0.295 s] [INFO] IGB Main (run me) .................................. SUCCESS [ 12.844 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:40 min [INFO] Finished at: 2023-12-13T15:58:29Z [INFO] ------------------------------------------------------------------------