+ umask 000 + GIT_LFS_SKIP_SMUDGE=1 retry 6 git clone --branch="IGBF-3113" --depth 50 https://x-token-auth:$REPOSITORY_OAUTH_ACCESS_TOKEN@bitbucket.org/$BITBUCKET_REPO_FULL_NAME.git $BUILD_DIR Cloning into '/opt/atlassian/pipelines/agent/build'... + git reset --hard a1f1a0e08ed4f03f6911b6f72de742d2722e4b3b HEAD is now at a1f1a0e IGBF-3113 Set up build environment using downloaded script + git config user.name bitbucket-pipelines + git config user.email commits-noreply@bitbucket.org + git config push.default current + git config http.${BITBUCKET_GIT_HTTP_ORIGIN}.proxy http://localhost:29418/ + git remote set-url origin http://bitbucket.org/$BITBUCKET_REPO_FULL_NAME + git reflog expire --expire=all --all + echo ".bitbucket/pipelines/generated" >> .git/info/exclude + chmod 777 $BUILD_DIR Cache "maven": Downloading Cache "maven": Downloaded 98.5 MiB in 6 seconds Cache "maven": Extracting Cache "maven": Extracted in 0 seconds Images used: build : docker.io/lorainelab/igb-maven-install4j@sha256:2597087095bb5c270110acb2ae94f8a15ef031f2db087dc3e31a3ecb1496a07d + curl -s -S -L -O https://${BB_AUTH_STRING}@api.bitbucket.org/2.0/repositories/lorainelab/iipc/src/master/env.sh + source env.sh + version=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout) + mvn install -P release-bitbucket-pipelines [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] IGB Project [INFO] Core - Heatmap Editor [INFO] Core - Affymetrix Common [INFO] Plugin - Sorting API and Impl [INFO] Plugin - Data caching API [INFO] Core - Synonym Lookup [INFO] Core - Genometry (Data Models) [INFO] Core - Preferences [INFO] Core - IGB Swing Extensions [INFO] Core - Genoviz Extensions [INFO] Core - IGB Services API [INFO] Core - Frame Manager [INFO] Core - Window Service [INFO] Core - JavaFX Utilities [INFO] Core - Menu API [INFO] Core - Context Menu Service [INFO] Core - IGB [INFO] Core - Bundle wrapper, deployer [INFO] Core - Logging Config [INFO] Core - Web Links [INFO] Plugin - Data caching GUI [INFO] Core - Quickload (data source) [INFO] Core - DAS (data source) [INFO] Plugin - Apollo Library [INFO] Plugin - Track Operations API, GUI [INFO] Plugin - Annotation Tab [INFO] Plugin - Console Tab [INFO] Plugin - Bigbed data format handler [INFO] Plugin - Bigwig data format handler [INFO] Plugin - Bookmarks and REST API [INFO] Plugin - External View [INFO] Plugin - Graph Tab [INFO] Plugin - Save Image GUI [INFO] Plugin - Script handler [INFO] Plugin - Keyword Search [INFO] Plugin - NCBI Blast [INFO] Plugin - Selection Info tab [INFO] Plugin - Restriction Sites tab [INFO] Plugin - Search Id or Props [INFO] Plugin - Advanced Search Tab [INFO] Plugin - Sequence Viewer GUI [INFO] Plugin - Survey GUI [INFO] Plugin - Graph thresholding visual analytics [INFO] Plugin - Update [INFO] Plugin - App Manager GUI [INFO] Plugin - Paired-end Read Preprocessor [INFO] Plugin - Save Session Manager [INFO] Plugin - Toolbar Preferences GUI [INFO] Plugin - Error reporting [INFO] Plugin - Feedback [INFO] Plugin - Narrowpeak data format handler [INFO] Plugin - File Handler - Genotyping Results [INFO] Plugin - BED file format handler [INFO] Plugin - BAM data format handler [INFO] Plugin - BAI index visualization handler [INFO] Plugin - App Store REST API [INFO] IGB Main (run me) [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building IGB Project 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ igb-project --- [INFO] Installing /opt/atlassian/pipelines/agent/build/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-project/9.1.10/igb-project-9.1.10.pom [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Heatmap Editor 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ heatmap-editor --- [INFO] Copying 0 resource [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ heatmap-editor --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 14 source files to /opt/atlassian/pipelines/agent/build/core/heatmap-editor/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ heatmap-editor --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ heatmap-editor --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ heatmap-editor --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ heatmap-editor --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ heatmap-editor --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/heatmap-editor/pom.xml to /root/.m2/repository/org/lorainelab/igb/heatmap-editor/9.1.10/heatmap-editor-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/heatmap-editor/target/heatmap-editor-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/heatmap-editor/9.1.10/heatmap-editor-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ heatmap-editor --- [INFO] Installing org/lorainelab/igb/heatmap-editor/9.1.10/heatmap-editor-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ heatmap-editor --- [INFO] Configured Artifact: org.lorainelab.igb:heatmap-editor:9.1.10:jar [INFO] Copying heatmap-editor-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/heatmap-editor-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Affymetrix Common 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ affymetrix-common --- [INFO] Copying 286 resources [INFO] The encoding used to copy filtered properties files have not been set. This means that the same encoding will be used to copy filtered properties files as when copying other filtered resources. This might not be what you want! Run your build with --debug to see which files might be affected. Read more at https://maven.apache.org/plugins/maven-resources-plugin/examples/filtering-properties-files.html [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ affymetrix-common --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /opt/atlassian/pipelines/agent/build/core/common/target/classes Note: /opt/atlassian/pipelines/agent/build/core/common/src/main/java/com/affymetrix/common/PreferenceUtils.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ affymetrix-common --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/common/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ affymetrix-common --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ affymetrix-common --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ affymetrix-common --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ affymetrix-common --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/common/pom.xml to /root/.m2/repository/org/lorainelab/igb/affymetrix-common/9.1.10/affymetrix-common-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/common/target/affymetrix-common-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/affymetrix-common/9.1.10/affymetrix-common-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ affymetrix-common --- [INFO] Installing org/lorainelab/igb/affymetrix-common/9.1.10/affymetrix-common-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ affymetrix-common --- [INFO] Configured Artifact: org.lorainelab.igb:affymetrix-common:9.1.10:jar [INFO] Copying affymetrix-common-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/affymetrix-common-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Sorting API and Impl 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ external-sort --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/external-sort/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ external-sort --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /opt/atlassian/pipelines/agent/build/plugins/external-sort/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/external-sort/src/main/java/org/lorainelab/igb/externalsort/api/ComparatorMetadata.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ external-sort --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ external-sort --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/external-sort/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ external-sort --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.externalsort.ExternalSortTest 21:03:07.276 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 21:03:07.291 [main] INFO o.l.i.externalsort.ExternalSortTest - 30.88 ms [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 s - in org.lorainelab.igb.externalsort.ExternalSortTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ external-sort --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ external-sort --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/external-sort/pom.xml to /root/.m2/repository/org/lorainelab/igb/external-sort/9.1.10/external-sort-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/external-sort/target/external-sort-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/external-sort/9.1.10/external-sort-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ external-sort --- [INFO] Installing org/lorainelab/igb/external-sort/9.1.10/external-sort-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ external-sort --- [INFO] Configured Artifact: org.lorainelab.igb:external-sort:9.1.10:jar [INFO] Copying external-sort-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/external-sort-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Data caching API 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ cache-api --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/cache-api/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ cache-api --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/cache-api/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ cache-api --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/cache-api/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ cache-api --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cache-api --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ cache-api --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ cache-api --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/cache-api/pom.xml to /root/.m2/repository/org/lorainelab/igb/cache-api/9.1.10/cache-api-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/cache-api/target/cache-api-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/cache-api/9.1.10/cache-api-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ cache-api --- [INFO] Installing org/lorainelab/igb/cache-api/9.1.10/cache-api-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ cache-api --- [INFO] Configured Artifact: org.lorainelab.igb:cache-api:9.1.10:jar [INFO] Copying cache-api-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/cache-api-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Synonym Lookup 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ synonym-lookup --- [INFO] Copying 0 resource [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ synonym-lookup --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 9 source files to /opt/atlassian/pipelines/agent/build/core/synonym-lookup/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ synonym-lookup --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ synonym-lookup --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/core/synonym-lookup/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ synonym-lookup --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.synonymlookup.test.SynonymLookupTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.159 s - in org.lorainelab.igb.synonymlookup.test.SynonymLookupTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ synonym-lookup --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ synonym-lookup --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/synonym-lookup/pom.xml to /root/.m2/repository/org/lorainelab/igb/synonym-lookup/9.1.10/synonym-lookup-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/synonym-lookup/target/synonym-lookup-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/synonym-lookup/9.1.10/synonym-lookup-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ synonym-lookup --- [INFO] Installing org/lorainelab/igb/synonym-lookup/9.1.10/synonym-lookup-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ synonym-lookup --- [INFO] Configured Artifact: org.lorainelab.igb:synonym-lookup:9.1.10:jar [INFO] Copying synonym-lookup-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/synonym-lookup-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Genometry (Data Models) 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ genometry --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ genometry --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 394 source files to /opt/atlassian/pipelines/agent/build/core/genometry/target/classes Note: /opt/atlassian/pipelines/agent/build/core/genometry/src/main/java/com/affymetrix/genometry/thread/CThreadWorker.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ genometry --- [INFO] Copying 61 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ genometry --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 28 source files to /opt/atlassian/pipelines/agent/build/core/genometry/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ genometry --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.affymetrix.genometry.NibbleBioSeqTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 s - in com.affymetrix.genometry.NibbleBioSeqTest [INFO] Running com.affymetrix.genometry.GFF3SymTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 s - in com.affymetrix.genometry.GFF3SymTest [INFO] Running com.affymetrix.genometry.BioSeqTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.affymetrix.genometry.BioSeqTest [INFO] Running com.affymetrix.genometry.comparator.SeqSymIdComparatorTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.affymetrix.genometry.comparator.SeqSymIdComparatorTest [INFO] Running com.affymetrix.genometry.parsers.GFF3ParserTest [WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.001 s - in com.affymetrix.genometry.parsers.GFF3ParserTest [INFO] Running com.affymetrix.genometry.parsers.TwoBitParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 s - in com.affymetrix.genometry.parsers.TwoBitParserTest [INFO] Running com.affymetrix.genometry.parsers.NibbleResiduesParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.affymetrix.genometry.parsers.NibbleResiduesParserTest [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: 0.038 s - in com.affymetrix.genometry.parsers.graph.ScoredIntervalParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.BgrParserTest 16, null, null [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in com.affymetrix.genometry.parsers.graph.BgrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.BarParserTest Aug 15, 2022 9:03:13 PM com.affymetrix.genometry.parsers.graph.BarParser getSeqGroup WARNING: Did not find genomeVersion Test Group:Test Group. Adding it as new genomeVersion [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in com.affymetrix.genometry.parsers.graph.BarParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.UseqParserTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in com.affymetrix.genometry.parsers.graph.UseqParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.SgrParserTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in com.affymetrix.genometry.parsers.graph.SgrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.GrParserTest loaded graph data, total points = 2 loaded graph data, total points = 2 loaded graph data, total points = 10 loaded graph data, total points = 10 loaded graph data, total points = 10 [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in com.affymetrix.genometry.parsers.graph.GrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.CntParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 s - in com.affymetrix.genometry.parsers.graph.CntParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.WiggleParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 s - in com.affymetrix.genometry.parsers.graph.WiggleParserTest [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: 0.003 s - in com.affymetrix.genometry.parsers.FastaParserTest [INFO] Running com.affymetrix.genometry.parsers.TrackLineParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in com.affymetrix.genometry.parsers.TrackLineParserTest [INFO] Running com.affymetrix.genometry.parsers.BrsParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in com.affymetrix.genometry.parsers.BrsParserTest [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: 0.01 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: 0.005 s - in com.affymetrix.genometry.parsers.Bprobe1ParserTest [INFO] Running com.affymetrix.genometry.parsers.NibbleFileParserTest Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 14 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 3 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 4 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 3 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 26 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 20 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 10 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 9 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 36 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 2 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 2 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 15 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 27 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 in NibbleIterator.stringToNibbles(), start >= end NOT YET IMPLEMENTED Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 in NibbleIterator.stringToNibbles(), start >= end NOT YET IMPLEMENTED Aug 15, 2022 9:03:14 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 s - in com.affymetrix.genometry.parsers.NibbleFileParserTest [INFO] Running com.affymetrix.genometry.parsers.TwoBitNewTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 s - in com.affymetrix.genometry.parsers.TwoBitNewTest [INFO] Running com.affymetrix.genometry.parsers.CytobandParserTest in CytobandParser.writeAnnotations() [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in com.affymetrix.genometry.parsers.CytobandParserTest [INFO] Running com.affymetrix.genometry.parsers.PSLParserTest [INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.162 s - in com.affymetrix.genometry.parsers.PSLParserTest [INFO] Running com.affymetrix.genometry.parsers.SamRecordFlagTest [INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in com.affymetrix.genometry.parsers.SamRecordFlagTest [INFO] Running com.affymetrix.genometry.parsers.BpsParserTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in com.affymetrix.genometry.parsers.BpsParserTest [INFO] Running com.affymetrix.genometry.util.IgbStringUtilsTest [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.105 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: 0.001 s - in com.affymetrix.genometry.util.SeqUtilsTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 80, Failures: 0, Errors: 0, Skipped: 6 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ genometry --- [WARNING] Bundle org.lorainelab.igb:genometry:bundle:9.1.10 : Export com.affymetrix.genometry.parsers.useq, has 1, private references [com.affymetrix.genometry.parsers.useq.data], [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ genometry --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/genometry/pom.xml to /root/.m2/repository/org/lorainelab/igb/genometry/9.1.10/genometry-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/genometry/target/genometry-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/genometry/9.1.10/genometry-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ genometry --- [INFO] Installing org/lorainelab/igb/genometry/9.1.10/genometry-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ genometry --- [INFO] Configured Artifact: org.lorainelab.igb:genometry:9.1.10:jar [INFO] Copying genometry-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/genometry-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Preferences 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igb-preferences --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igb-preferences --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /opt/atlassian/pipelines/agent/build/core/igb-preferences/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igb-preferences --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igb-preferences --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/core/igb-preferences/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igb-preferences --- [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: 0.295 s - in com.lorainelab.igb.preferences.IgbPreferencesParseTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igb-preferences --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igb-preferences --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-preferences/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-preferences/9.1.10/igb-preferences-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-preferences/target/igb-preferences-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igb-preferences/9.1.10/igb-preferences-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igb-preferences --- [INFO] Installing org/lorainelab/igb/igb-preferences/9.1.10/igb-preferences-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igb-preferences --- [INFO] Configured Artifact: org.lorainelab.igb:igb-preferences:9.1.10:jar [INFO] Copying igb-preferences-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igb-preferences-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - IGB Swing Extensions 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igbSwingExt --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/igb-swing-ext/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igbSwingExt --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 41 source files to /opt/atlassian/pipelines/agent/build/core/igb-swing-ext/target/classes Note: /opt/atlassian/pipelines/agent/build/core/igb-swing-ext/src/main/java/com/affymetrix/igb/swing/JRPComboBox.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:manifest (bundle-manifest) @ igbSwingExt --- [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igbSwingExt --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/igb-swing-ext/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igbSwingExt --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igbSwingExt --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igbSwingExt --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igbSwingExt --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-swing-ext/pom.xml to /root/.m2/repository/org/lorainelab/igb/igbSwingExt/9.1.10/igbSwingExt-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-swing-ext/target/igbSwingExt-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igbSwingExt/9.1.10/igbSwingExt-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igbSwingExt --- [INFO] Installing org/lorainelab/igb/igbSwingExt/9.1.10/igbSwingExt-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igbSwingExt --- [INFO] Configured Artifact: org.lorainelab.igb:igbSwingExt:9.1.10:jar [INFO] Copying igbSwingExt-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igbSwingExt-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Genoviz Extensions 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igb-genoviz-extensions --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igb-genoviz-extensions --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 10 source files to /opt/atlassian/pipelines/agent/build/core/igb-genoviz-ext/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igb-genoviz-extensions --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/igb-genoviz-ext/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igb-genoviz-extensions --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igb-genoviz-extensions --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igb-genoviz-extensions --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igb-genoviz-extensions --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-genoviz-ext/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-genoviz-extensions/9.1.10/igb-genoviz-extensions-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-genoviz-ext/target/igb-genoviz-extensions-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igb-genoviz-extensions/9.1.10/igb-genoviz-extensions-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igb-genoviz-extensions --- [INFO] Installing org/lorainelab/igb/igb-genoviz-extensions/9.1.10/igb-genoviz-extensions-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igb-genoviz-extensions --- [INFO] Configured Artifact: org.lorainelab.igb:igb-genoviz-extensions:9.1.10:jar [INFO] Copying igb-genoviz-extensions-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igb-genoviz-extensions-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - IGB Services API 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igb-services --- [INFO] Copying 0 resource [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igb-services --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 20 source files to /opt/atlassian/pipelines/agent/build/core/igb-services-api/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igb-services --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igb-services --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igb-services --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igb-services --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igb-services --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-services-api/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-services/9.1.10/igb-services-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-services-api/target/igb-services-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igb-services/9.1.10/igb-services-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igb-services --- [INFO] Installing org/lorainelab/igb/igb-services/9.1.10/igb-services-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igb-services --- [INFO] Configured Artifact: org.lorainelab.igb:igb-services:9.1.10:jar [INFO] Copying igb-services-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igb-services-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Frame Manager 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ frameManager --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ frameManager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/core/frameManager/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ frameManager --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/frameManager/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ frameManager --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ frameManager --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ frameManager --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ frameManager --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/frameManager/pom.xml to /root/.m2/repository/org/lorainelab/igb/frameManager/9.1.10/frameManager-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/frameManager/target/frameManager-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/frameManager/9.1.10/frameManager-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ frameManager --- [INFO] Installing org/lorainelab/igb/frameManager/9.1.10/frameManager-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ frameManager --- [INFO] Configured Artifact: org.lorainelab.igb:frameManager:9.1.10:jar [INFO] Copying frameManager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/frameManager-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Window Service 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ window-service --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ window-service --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /opt/atlassian/pipelines/agent/build/core/window-service/target/classes Note: /opt/atlassian/pipelines/agent/build/core/window-service/src/main/java/com/affymetrix/igb/window/service/def/WindowServiceDefaultImpl.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ window-service --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ window-service --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ window-service --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ window-service --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ window-service --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/window-service/pom.xml to /root/.m2/repository/org/lorainelab/igb/window-service/9.1.10/window-service-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/window-service/target/window-service-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/window-service/9.1.10/window-service-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ window-service --- [INFO] Installing org/lorainelab/igb/window-service/9.1.10/window-service-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ window-service --- [INFO] Configured Artifact: org.lorainelab.igb:window-service:9.1.10:jar [INFO] Copying window-service-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/window-service-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - JavaFX Utilities 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igb-javafx-util --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/igb-javafx-util/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igb-javafx-util --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/core/igb-javafx-util/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igb-javafx-util --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/igb-javafx-util/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igb-javafx-util --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igb-javafx-util --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igb-javafx-util --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igb-javafx-util --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-javafx-util/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb-javafx-util/9.1.10/igb-javafx-util-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb-javafx-util/target/igb-javafx-util-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igb-javafx-util/9.1.10/igb-javafx-util-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igb-javafx-util --- [INFO] Installing org/lorainelab/igb/igb-javafx-util/9.1.10/igb-javafx-util-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igb-javafx-util --- [INFO] Configured Artifact: org.lorainelab.igb:igb-javafx-util:9.1.10:jar [INFO] Copying igb-javafx-util-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igb-javafx-util-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Menu API 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ org.lorainelab.igb.menu.api --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/menu-api/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ org.lorainelab.igb.menu.api --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 13 source files to /opt/atlassian/pipelines/agent/build/core/menu-api/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ org.lorainelab.igb.menu.api --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/menu-api/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ org.lorainelab.igb.menu.api --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ org.lorainelab.igb.menu.api --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ org.lorainelab.igb.menu.api --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ org.lorainelab.igb.menu.api --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/menu-api/pom.xml to /root/.m2/repository/org/lorainelab/igb/org.lorainelab.igb.menu.api/9.1.10/org.lorainelab.igb.menu.api-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/menu-api/target/org.lorainelab.igb.menu.api-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/org.lorainelab.igb.menu.api/9.1.10/org.lorainelab.igb.menu.api-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ org.lorainelab.igb.menu.api --- [INFO] Installing org/lorainelab/igb/org.lorainelab.igb.menu.api/9.1.10/org.lorainelab.igb.menu.api-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ org.lorainelab.igb.menu.api --- [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.menu.api:9.1.10:jar [INFO] Copying org.lorainelab.igb.menu.api-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.menu.api-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Context Menu Service 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ context-menu-service --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/context-menu-service/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ context-menu-service --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/core/context-menu-service/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ context-menu-service --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/context-menu-service/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ context-menu-service --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ context-menu-service --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ context-menu-service --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ context-menu-service --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/context-menu-service/pom.xml to /root/.m2/repository/org/lorainelab/igb/context-menu-service/9.1.10/context-menu-service-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/context-menu-service/target/context-menu-service-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/context-menu-service/9.1.10/context-menu-service-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ context-menu-service --- [INFO] Installing org/lorainelab/igb/context-menu-service/9.1.10/context-menu-service-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ context-menu-service --- [INFO] Configured Artifact: org.lorainelab.igb:context-menu-service:9.1.10:jar [INFO] Copying context-menu-service-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/context-menu-service-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - IGB 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- git-commit-id-plugin:2.1.4:revision (default) @ igb --- [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igb --- [INFO] Copying 12 resources [INFO] Copying 48 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 336 source files to /opt/atlassian/pipelines/agent/build/core/igb/target/classes Note: /opt/atlassian/pipelines/agent/build/core/igb/src/main/java/com/affymetrix/igb/IgbServiceImpl.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igb --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/core/igb/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igb --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igb --- [WARNING] Bundle org.lorainelab.igb:igb:bundle:9.1.10 : Export com.affymetrix.igb.shared, has 2, private references [com.affymetrix.igb.action, com.affymetrix.igb.tiers], [WARNING] Bundle org.lorainelab.igb:igb:bundle:9.1.10 : Export com.affymetrix.igb.view.load, has 2, private references [com.affymetrix.igb.view, com.affymetrix.igb.tiers], [WARNING] Bundle org.lorainelab.igb:igb:bundle:9.1.10 : Export com.affymetrix.igb.view.factories, has 3, private references [com.affymetrix.igb.view.layout, com.affymetrix.igb.view, com.affymetrix.igb.services.registry], [WARNING] Bundle org.lorainelab.igb:igb:bundle:9.1.10 : Export com.affymetrix.igb.glyph, has 1, private references [com.affymetrix.igb.view], [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igb --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb/pom.xml to /root/.m2/repository/org/lorainelab/igb/igb/9.1.10/igb-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/igb/target/igb-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igb/9.1.10/igb-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igb --- [INFO] Installing org/lorainelab/igb/igb/9.1.10/igb-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igb --- [INFO] Configured Artifact: org.lorainelab.igb:igb:9.1.10:jar [INFO] Copying igb-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igb-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Bundle wrapper, deployer 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ shared-lib-wrapper --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/shared-lib-wrapper/src/main/java [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/shared-lib-wrapper/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ shared-lib-wrapper --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ shared-lib-wrapper --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/shared-lib-wrapper/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ shared-lib-wrapper --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ shared-lib-wrapper --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ shared-lib-wrapper --- [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:9.1.10 : Unused Export-Package instructions: [affymetrix.calvin.*, affymetrix.fusion.*, affymetrix.gcos.*, org.jdesktop.swingx.*, com.boxysystems.jgoogleanalytics.*] [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:9.1.10 : 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:9.1.10 : Export org.freehep.graphicsbase.util, has 1, private references [junit.framework], [WARNING] Bundle org.lorainelab.igb:shared-lib-wrapper:bundle:9.1.10 : Export org.freehep.graphicsio.test, has 1, private references [junit.framework], [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ shared-lib-wrapper --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/shared-lib-wrapper/pom.xml to /root/.m2/repository/org/lorainelab/igb/shared-lib-wrapper/9.1.10/shared-lib-wrapper-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/shared-lib-wrapper/target/shared-lib-wrapper-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/shared-lib-wrapper/9.1.10/shared-lib-wrapper-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ shared-lib-wrapper --- [INFO] Installing org/lorainelab/igb/shared-lib-wrapper/9.1.10/shared-lib-wrapper-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.8:copy (copy) @ shared-lib-wrapper --- [INFO] Configured Artifact: com.google.guava:guava:16.0.1:jar [INFO] Configured Artifact: org.apache.commons:commons-lang3:3.4:jar [INFO] Configured Artifact: org.apache.commons:commons-csv:1.2:jar [INFO] Configured Artifact: commons-io:commons-io:2.4:jar [INFO] Configured Artifact: com.affymetrix:genoviz:1.1.9:jar [INFO] Configured Artifact: org.lorainelab.igb:shared-lib-wrapper:9.1.10:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.main:5.2.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.scr:1.8.2:jar [INFO] Configured Artifact: org.osgi:org.osgi.compendium:5.0.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.bundlerepository:2.0.10:jar [INFO] Configured Artifact: org.broad.igv:bigwig:2.0.0:jar [INFO] Configured Artifact: org.apache.commons:commons-compress:1.5:jar [INFO] Configured Artifact: commons-codec:commons-codec:1.6:jar [INFO] Configured Artifact: commons-pool:commons-pool:1.6:jar [INFO] Configured Artifact: commons-logging:commons-logging:1.2:jar [INFO] Configured Artifact: org.apache.commons:commons-jexl:2.1.1:jar [INFO] Configured Artifact: com.jidesoft:jide-ultimate:3.5.15:jar [INFO] Configured Artifact: com.google.code.gson:gson:2.3.1:jar [INFO] Configured Artifact: org.slf4j:slf4j-api:1.7.7:jar [INFO] Configured Artifact: ch.qos.logback:logback-core:1.1.2:jar [INFO] Configured Artifact: ch.qos.logback:logback-classic:1.1.2:jar [INFO] Configured Artifact: htsjdk-igb:htsjdk-igb:2.16.3:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.http.bundle:2.3.2:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.configadmin:1.8.8:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.fileinstall:3.5.0:jar [INFO] Configured Artifact: com.github.kevinsawicki:http-request:6.0:jar [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:1.0.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.gogo.runtime:0.16.2:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.gogo.shell:0.12.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.gogo.command:0.16.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.shell.remote:1.1.2:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.dependencymanager:3.2.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.dependencymanager.shell:3.2.0:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.http.servlet-api:?:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.http.jetty:4.0.10:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.log:1.0.1:jar [INFO] Configured Artifact: org.osgi:org.osgi.service.remoteserviceadmin:1.1.0:jar [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.remote.services.commons:1.0.0:jar [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.remote.services.discovery.provider.configured:1.0.0:jar [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.remote.services.topology.manager:1.0.0:jar [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.remote.services.distribution.provider.http:1.0.0:jar [INFO] Configured Artifact: com.fasterxml.jackson.core:jackson-core:2.3.5:jar [INFO] Configured Artifact: com.fasterxml.jackson.core:jackson-annotations:2.3.5:jar [INFO] Configured Artifact: com.fasterxml.jackson.core:jackson-databind:2.3.5:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.webconsole:4.3.12:jar [INFO] Configured Artifact: commons-fileupload:commons-fileupload:1.4:jar [INFO] Configured Artifact: org.apache.felix:org.apache.felix.eventadmin:1.5.0:jar [INFO] Copying guava-16.0.1.jar to /opt/atlassian/pipelines/agent/build/bundles/guava-16.0.1.jar [INFO] Copying commons-lang3-3.4.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-lang3-3.4.jar [INFO] Copying commons-csv-1.2.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-csv-1.2.jar [INFO] Copying commons-io-2.4.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-io-2.4.jar [INFO] Copying genoviz-1.1.9.jar to /opt/atlassian/pipelines/agent/build/bundles/genoviz-1.1.9.jar [INFO] Copying shared-lib-wrapper-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/shared-lib-wrapper-9.1.10.jar [INFO] Copying org.apache.felix.main-5.2.0.jar to /opt/atlassian/pipelines/agent/build/bundles/felix.jar [INFO] Copying org.apache.felix.scr-1.8.2.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.scr-1.8.2.jar [INFO] Copying org.osgi.compendium-5.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.osgi.compendium-5.0.0.jar [INFO] Copying org.apache.felix.bundlerepository-2.0.10.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.bundlerepository-2.0.10.jar [INFO] Copying bigwig-2.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/bigwig-2.0.0.jar [INFO] Copying commons-compress-1.5.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-compress-1.5.jar [INFO] Copying commons-codec-1.6.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-codec-1.6.jar [INFO] Copying commons-pool-1.6.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-pool-1.6.jar [INFO] Copying commons-logging-1.2.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-logging-1.2.jar [INFO] Copying commons-jexl-2.1.1.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-jexl-2.1.1.jar [INFO] Copying jide-ultimate-3.5.15.jar to /opt/atlassian/pipelines/agent/build/bundles/jide-ultimate-3.5.15.jar [INFO] Copying gson-2.3.1.jar to /opt/atlassian/pipelines/agent/build/bundles/gson-2.3.1.jar [INFO] Copying slf4j-api-1.7.7.jar to /opt/atlassian/pipelines/agent/build/bundles/slf4j-api-1.7.7.jar [INFO] Copying logback-core-1.1.2.jar to /opt/atlassian/pipelines/agent/build/bundles/logback-core-1.1.2.jar [INFO] Copying logback-classic-1.1.2.jar to /opt/atlassian/pipelines/agent/build/bundles/logback-classic-1.1.2.jar [INFO] Copying htsjdk-igb-2.16.3.jar to /opt/atlassian/pipelines/agent/build/bundles/htsjdk-igb-2.16.3.jar [INFO] Copying org.apache.felix.http.bundle-2.3.2.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.http.bundle-2.3.2.jar [INFO] Copying org.apache.felix.configadmin-1.8.8.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.configadmin-1.8.8.jar [INFO] Copying org.apache.felix.fileinstall-3.5.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.fileinstall-3.5.0.jar [INFO] Copying http-request-6.0.jar to /opt/atlassian/pipelines/agent/build/bundles/http-request-6.0.jar [INFO] Copying org.lorainelab.igb.error.reporter.api-1.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.error.reporter.api-1.0.0.jar [INFO] Copying org.apache.felix.gogo.runtime-0.16.2.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.gogo.runtime-0.16.2.jar [INFO] Copying org.apache.felix.gogo.shell-0.12.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.gogo.shell-0.12.0.jar [INFO] Copying org.apache.felix.gogo.command-0.16.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.gogo.command-0.16.0.jar [INFO] Copying org.apache.felix.shell.remote-1.1.2.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.shell.remote-1.1.2.jar [INFO] Copying org.apache.felix.dependencymanager-3.2.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.dependencymanager-3.2.0.jar [INFO] Copying org.apache.felix.dependencymanager.shell-3.2.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.dependencymanager.shell-3.2.0.jar [INFO] Copying org.apache.felix.http.servlet-api-1.1.2.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.http.servlet-api-1.1.2.jar [INFO] Copying org.apache.felix.http.jetty-4.0.10.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.http.jetty-4.0.10.jar [INFO] Copying org.apache.felix.log-1.0.1.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.log-1.0.1.jar [INFO] Copying org.osgi.service.remoteserviceadmin-1.1.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.osgi.service.remoteserviceadmin-1.1.0.jar [INFO] Copying org.lorainelab.igb.remote.services.commons-1.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.remote.services.commons-1.0.0.jar [INFO] Copying org.lorainelab.igb.remote.services.discovery.provider.configured-1.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.remote.services.discovery.provider.configured-1.0.0.jar [INFO] Copying org.lorainelab.igb.remote.services.topology.manager-1.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.remote.services.topology.manager-1.0.0.jar [INFO] Copying org.lorainelab.igb.remote.services.distribution.provider.http-1.0.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.remote.services.distribution.provider.http-1.0.0.jar [INFO] Copying jackson-core-2.3.5.jar to /opt/atlassian/pipelines/agent/build/bundles/jackson-core-2.3.5.jar [INFO] Copying jackson-annotations-2.3.5.jar to /opt/atlassian/pipelines/agent/build/bundles/jackson-annotations-2.3.5.jar [INFO] Copying jackson-databind-2.3.5.jar to /opt/atlassian/pipelines/agent/build/bundles/jackson-databind-2.3.5.jar [INFO] Copying org.apache.felix.webconsole-4.3.12.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.webconsole-4.3.12.jar [INFO] Copying commons-fileupload-1.4.jar to /opt/atlassian/pipelines/agent/build/bundles/commons-fileupload-1.4.jar [INFO] Copying org.apache.felix.eventadmin-1.5.0.jar to /opt/atlassian/pipelines/agent/build/bundles/org.apache.felix.eventadmin-1.5.0.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Logging Config 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ logging-config --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/logging-config/src/main/java [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ logging-config --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ logging-config --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/logging-config/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ logging-config --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ logging-config --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ logging-config --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ logging-config --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/logging-config/pom.xml to /root/.m2/repository/org/lorainelab/igb/logging-config/9.1.10/logging-config-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/logging-config/target/logging-config-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/logging-config/9.1.10/logging-config-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ logging-config --- [INFO] Installing org/lorainelab/igb/logging-config/9.1.10/logging-config-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ logging-config --- [INFO] Configured Artifact: org.lorainelab.igb:logging-config:9.1.10:jar [INFO] Copying logging-config-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/logging-config-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Web Links 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ weblinks --- [INFO] Copying 0 resource [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ weblinks --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 10 source files to /opt/atlassian/pipelines/agent/build/core/weblinks/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ weblinks --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/weblinks/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ weblinks --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ weblinks --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ weblinks --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ weblinks --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/weblinks/pom.xml to /root/.m2/repository/org/lorainelab/igb/weblinks/9.1.10/weblinks-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/weblinks/target/weblinks-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/weblinks/9.1.10/weblinks-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ weblinks --- [INFO] Installing org/lorainelab/igb/weblinks/9.1.10/weblinks-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ weblinks --- [INFO] Configured Artifact: org.lorainelab.igb:weblinks:9.1.10:jar [INFO] Copying weblinks-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/weblinks-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Data caching GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ cache --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/cache/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ cache --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/cache/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ cache --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ cache --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/cache/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ cache --- [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: 0.037 s - in com.lorainelab.cache.disk.RemoteFileCacheServiceTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 8, Failures: 0, Errors: 0, Skipped: 8 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ cache --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ cache --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/cache/pom.xml to /root/.m2/repository/org/lorainelab/igb/cache/9.1.10/cache-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/cache/target/cache-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/cache/9.1.10/cache-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ cache --- [INFO] Installing org/lorainelab/igb/cache/9.1.10/cache-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ cache --- [INFO] Configured Artifact: org.lorainelab.igb:cache:9.1.10:jar [INFO] Copying cache-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/cache-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - Quickload (data source) 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ quickload --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ quickload --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /opt/atlassian/pipelines/agent/build/core/quickload/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ quickload --- [INFO] Copying 9 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ quickload --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/core/quickload/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ quickload --- [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: 0.186 s - in org.lorainelab.igb.quickload.utils.AnnotsParserTest [INFO] Running org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest Aug 15, 2022 9:03:28 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. 21:03:28.918 [main] INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server file:/opt/atlassian/pipelines/agent/build/core/quickload/target/test-classes/quickload/ 21:03:28.935 [main] WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from file:/opt/atlassian/pipelines/agent/build/core/quickload/target/test-classes/quickload/synonyms.txt 21:03:28.936 [main] WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: file:/opt/atlassian/pipelines/agent/build/core/quickload/target/test-classes/quickload/species.txt [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 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: 0.011 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] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ quickload --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ quickload --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/quickload/pom.xml to /root/.m2/repository/org/lorainelab/igb/quickload/9.1.10/quickload-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/quickload/target/quickload-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/quickload/9.1.10/quickload-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ quickload --- [INFO] Installing org/lorainelab/igb/quickload/9.1.10/quickload-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ quickload --- [INFO] Configured Artifact: org.lorainelab.igb:quickload:9.1.10:jar [INFO] Copying quickload-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/quickload-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Core - DAS (data source) 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ das --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/core/das/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ das --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 33 source files to /opt/atlassian/pipelines/agent/build/core/das/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ das --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ das --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/core/das/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ das --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.lorainelab.das.DasDataProviderTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.756 s - in com.lorainelab.das.DasDataProviderTest [INFO] Running com.lorainelab.das.DasServerInfoTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.004 s - in com.lorainelab.das.DasServerInfoTest [INFO] Running com.lorainelab.das.DASFeatureParserTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 s - in com.lorainelab.das.DASFeatureParserTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 5 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ das --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ das --- [INFO] Installing /opt/atlassian/pipelines/agent/build/core/das/pom.xml to /root/.m2/repository/org/lorainelab/igb/das/9.1.10/das-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/core/das/target/das-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/das/9.1.10/das-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ das --- [INFO] Installing org/lorainelab/igb/das/9.1.10/das-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ das --- [INFO] Configured Artifact: org.lorainelab.igb:das:9.1.10:jar [INFO] Copying das-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/das-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Apollo Library 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ apollo-library --- [INFO] Copying 0 resource [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ apollo-library --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 17 source files to /opt/atlassian/pipelines/agent/build/plugins/ApolloLibrary/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ apollo-library --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ apollo-library --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ apollo-library --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ apollo-library --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ apollo-library --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/ApolloLibrary/pom.xml to /root/.m2/repository/org/lorainelab/igb/apollo-library/9.1.10/apollo-library-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/ApolloLibrary/target/apollo-library-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/apollo-library/9.1.10/apollo-library-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ apollo-library --- [INFO] Installing org/lorainelab/igb/apollo-library/9.1.10/apollo-library-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ apollo-library --- [INFO] Configured Artifact: org.lorainelab.igb:apollo-library:9.1.10:jar [INFO] Copying apollo-library-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/apollo-library-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Track Operations API, GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ track-operations-panel --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ track-operations-panel --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /opt/atlassian/pipelines/agent/build/plugins/track-operations-panel/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/track-operations-panel/src/main/java/org/lorainelab/igb/track/operations/api/OperationsPanel.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ track-operations-panel --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ track-operations-panel --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ track-operations-panel --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ track-operations-panel --- [WARNING] Bundle org.lorainelab.igb:track-operations-panel:bundle:9.1.10 : Export org.lorainelab.igb.track.operations.api, has 1, private references [org.lorainelab.igb.track.operations], [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ track-operations-panel --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/track-operations-panel/pom.xml to /root/.m2/repository/org/lorainelab/igb/track-operations-panel/9.1.10/track-operations-panel-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/track-operations-panel/target/track-operations-panel-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/track-operations-panel/9.1.10/track-operations-panel-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ track-operations-panel --- [INFO] Installing org/lorainelab/igb/track-operations-panel/9.1.10/track-operations-panel-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ track-operations-panel --- [INFO] Configured Artifact: org.lorainelab.igb:track-operations-panel:9.1.10:jar [INFO] Copying track-operations-panel-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/track-operations-panel-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Annotation Tab 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ annotation-tab --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ annotation-tab --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/AnnotationTab/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/AnnotationTab/src/main/java/com/affymetrix/igb/tabs/annotation/AnnotationPanelImpl.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ annotation-tab --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ annotation-tab --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ annotation-tab --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ annotation-tab --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ annotation-tab --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/AnnotationTab/pom.xml to /root/.m2/repository/org/lorainelab/igb/annotation-tab/9.1.10/annotation-tab-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/AnnotationTab/target/annotation-tab-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/annotation-tab/9.1.10/annotation-tab-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ annotation-tab --- [INFO] Installing org/lorainelab/igb/annotation-tab/9.1.10/annotation-tab-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ annotation-tab --- [INFO] Configured Artifact: org.lorainelab.igb:annotation-tab:9.1.10:jar [INFO] Copying annotation-tab-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/annotation-tab-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Console Tab 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ console-tab --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ console-tab --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/ConsoleTab/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ console-tab --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ console-tab --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ console-tab --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ console-tab --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ console-tab --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/ConsoleTab/pom.xml to /root/.m2/repository/org/lorainelab/igb/console-tab/9.1.10/console-tab-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/ConsoleTab/target/console-tab-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/console-tab/9.1.10/console-tab-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ console-tab --- [INFO] Installing org/lorainelab/igb/console-tab/9.1.10/console-tab-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ console-tab --- [INFO] Configured Artifact: org.lorainelab.igb:console-tab:9.1.10:jar [INFO] Copying console-tab-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/console-tab-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Bigbed data format handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bigBedHandler --- [INFO] Copying 0 resource [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ bigBedHandler --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/BigBedHandler/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bigBedHandler --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ bigBedHandler --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ bigBedHandler --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ bigBedHandler --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ bigBedHandler --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/BigBedHandler/pom.xml to /root/.m2/repository/org/lorainelab/igb/bigBedHandler/9.1.10/bigBedHandler-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/BigBedHandler/target/bigBedHandler-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/bigBedHandler/9.1.10/bigBedHandler-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ bigBedHandler --- [INFO] Installing org/lorainelab/igb/bigBedHandler/9.1.10/bigBedHandler-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ bigBedHandler --- [INFO] Configured Artifact: org.lorainelab.igb:bigBedHandler:9.1.10:jar [INFO] Copying bigBedHandler-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/bigBedHandler-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Bigwig data format handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bigWigHandler --- [INFO] Copying 0 resource [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ bigWigHandler --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/BigWigHandler/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bigWigHandler --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ bigWigHandler --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ bigWigHandler --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ bigWigHandler --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ bigWigHandler --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/BigWigHandler/pom.xml to /root/.m2/repository/org/lorainelab/igb/bigWigHandler/9.1.10/bigWigHandler-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/BigWigHandler/target/bigWigHandler-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/bigWigHandler/9.1.10/bigWigHandler-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ bigWigHandler --- [INFO] Installing org/lorainelab/igb/bigWigHandler/9.1.10/bigWigHandler-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ bigWigHandler --- [INFO] Configured Artifact: org.lorainelab.igb:bigWigHandler:9.1.10:jar [INFO] Copying bigWigHandler-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/bigWigHandler-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Bookmarks and REST API 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bookmark --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ bookmark --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 32 source files to /opt/atlassian/pipelines/agent/build/plugins/Bookmark/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/Activator.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: /opt/atlassian/pipelines/agent/build/plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkController.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bookmark --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ bookmark --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/Bookmark/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ bookmark --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.affymetrix.igb.bookmarks.BookMarkTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 s - in com.affymetrix.igb.bookmarks.BookMarkTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ bookmark --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ bookmark --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Bookmark/pom.xml to /root/.m2/repository/org/lorainelab/igb/bookmark/9.1.10/bookmark-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Bookmark/target/bookmark-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/bookmark/9.1.10/bookmark-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ bookmark --- [INFO] Installing org/lorainelab/igb/bookmark/9.1.10/bookmark-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ bookmark --- [INFO] Configured Artifact: org.lorainelab.igb:bookmark:9.1.10:jar [INFO] Copying bookmark-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/bookmark-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - External View 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ externalView --- [INFO] Copying 0 resource [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ externalView --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 12 source files to /opt/atlassian/pipelines/agent/build/plugins/ExternalView/target/classes Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ externalView --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ externalView --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/ExternalView/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ externalView --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running com.affymetrix.igb.external.EndPointTest [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.877 s - in com.affymetrix.igb.external.EndPointTest [INFO] Running com.affymetrix.igb.external.LoaderTest 21:03:35.114 INFO c.a.igb.external.ENSEMBLoader - Made URL string: {0} [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.138 s - in com.affymetrix.igb.external.LoaderTest [INFO] [INFO] Results: [INFO] [WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 1 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ externalView --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ externalView --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/ExternalView/pom.xml to /root/.m2/repository/org/lorainelab/igb/externalView/9.1.10/externalView-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/ExternalView/target/externalView-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/externalView/9.1.10/externalView-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ externalView --- [INFO] Installing org/lorainelab/igb/externalView/9.1.10/externalView-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ externalView --- [INFO] Configured Artifact: org.lorainelab.igb:externalView:9.1.10:jar [INFO] Copying externalView-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/externalView-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Graph Tab 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ graphTab --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ graphTab --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /opt/atlassian/pipelines/agent/build/plugins/GraphTab/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ graphTab --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ graphTab --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ graphTab --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ graphTab --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ graphTab --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/GraphTab/pom.xml to /root/.m2/repository/org/lorainelab/igb/graphTab/9.1.10/graphTab-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/GraphTab/target/graphTab-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/graphTab/9.1.10/graphTab-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ graphTab --- [INFO] Installing org/lorainelab/igb/graphTab/9.1.10/graphTab-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ graphTab --- [INFO] Configured Artifact: org.lorainelab.igb:graphTab:9.1.10:jar [INFO] Copying graphTab-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/graphTab-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Save Image GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ image-exporter --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ image-exporter --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 9 source files to /opt/atlassian/pipelines/agent/build/plugins/image-exporter/target/classes Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ image-exporter --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/image-exporter/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ image-exporter --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/image-exporter/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ image-exporter --- [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] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ image-exporter --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ image-exporter --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/image-exporter/pom.xml to /root/.m2/repository/org/lorainelab/igb/image-exporter/9.1.10/image-exporter-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/image-exporter/target/image-exporter-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/image-exporter/9.1.10/image-exporter-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ image-exporter --- [INFO] Installing org/lorainelab/igb/image-exporter/9.1.10/image-exporter-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ image-exporter --- [INFO] Configured Artifact: org.lorainelab.igb:image-exporter:9.1.10:jar [INFO] Copying image-exporter-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/image-exporter-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Script handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ igbScript --- [INFO] Copying 0 resource [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ igbScript --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/IGBScript/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ igbScript --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ igbScript --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ igbScript --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ igbScript --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ igbScript --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/IGBScript/pom.xml to /root/.m2/repository/org/lorainelab/igb/igbScript/9.1.10/igbScript-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/IGBScript/target/igbScript-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/igbScript/9.1.10/igbScript-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ igbScript --- [INFO] Installing org/lorainelab/igb/igbScript/9.1.10/igbScript-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ igbScript --- [INFO] Configured Artifact: org.lorainelab.igb:igbScript:9.1.10:jar [INFO] Copying igbScript-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/igbScript-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Keyword Search 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ keyWordSearch --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ keyWordSearch --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/KeyWordSearch/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ keyWordSearch --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ keyWordSearch --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ keyWordSearch --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ keyWordSearch --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ keyWordSearch --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/KeyWordSearch/pom.xml to /root/.m2/repository/org/lorainelab/igb/keyWordSearch/9.1.10/keyWordSearch-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/KeyWordSearch/target/keyWordSearch-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/keyWordSearch/9.1.10/keyWordSearch-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ keyWordSearch --- [INFO] Installing org/lorainelab/igb/keyWordSearch/9.1.10/keyWordSearch-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ keyWordSearch --- [INFO] Configured Artifact: org.lorainelab.igb:keyWordSearch:9.1.10:jar [INFO] Copying keyWordSearch-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/keyWordSearch-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - NCBI Blast 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ ncbiBlast --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ ncbiBlast --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 11 source files to /opt/atlassian/pipelines/agent/build/plugins/NCBIBlast/target/classes Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ ncbiBlast --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ ncbiBlast --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/NCBIBlast/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ ncbiBlast --- [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: 2.216 s - in apollo.analysis.RemoteBlastNCBITest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ ncbiBlast --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ ncbiBlast --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/NCBIBlast/pom.xml to /root/.m2/repository/org/lorainelab/igb/ncbiBlast/9.1.10/ncbiBlast-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/NCBIBlast/target/ncbiBlast-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/ncbiBlast/9.1.10/ncbiBlast-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ ncbiBlast --- [INFO] Installing org/lorainelab/igb/ncbiBlast/9.1.10/ncbiBlast-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ ncbiBlast --- [INFO] Configured Artifact: org.lorainelab.igb:ncbiBlast:9.1.10:jar [INFO] Copying ncbiBlast-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/ncbiBlast-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Selection Info tab 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ propertyView --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ propertyView --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/PropertyView/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ propertyView --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ propertyView --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ propertyView --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ propertyView --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ propertyView --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/PropertyView/pom.xml to /root/.m2/repository/org/lorainelab/igb/propertyView/9.1.10/propertyView-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/PropertyView/target/propertyView-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/propertyView/9.1.10/propertyView-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ propertyView --- [INFO] Installing org/lorainelab/igb/propertyView/9.1.10/propertyView-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ propertyView --- [INFO] Configured Artifact: org.lorainelab.igb:propertyView:9.1.10:jar [INFO] Copying propertyView-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/propertyView-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Restriction Sites tab 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ restrictionSites --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ restrictionSites --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/RestrictionSites/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/RestrictionSites/src/main/java/com/affymetrix/igb/restrictions/RestrictionControlView.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ restrictionSites --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ restrictionSites --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ restrictionSites --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ restrictionSites --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ restrictionSites --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/RestrictionSites/pom.xml to /root/.m2/repository/org/lorainelab/igb/restrictionSites/9.1.10/restrictionSites-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/RestrictionSites/target/restrictionSites-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/restrictionSites/9.1.10/restrictionSites-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ restrictionSites --- [INFO] Installing org/lorainelab/igb/restrictionSites/9.1.10/restrictionSites-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ restrictionSites --- [INFO] Configured Artifact: org.lorainelab.igb:restrictionSites:9.1.10:jar [INFO] Copying restrictionSites-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/restrictionSites-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Search Id or Props 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ searchModelIdOrProps --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ searchModelIdOrProps --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /opt/atlassian/pipelines/agent/build/plugins/SearchModeIdOrProps/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ searchModelIdOrProps --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ searchModelIdOrProps --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ searchModelIdOrProps --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ searchModelIdOrProps --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ searchModelIdOrProps --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/SearchModeIdOrProps/pom.xml to /root/.m2/repository/org/lorainelab/igb/searchModelIdOrProps/9.1.10/searchModelIdOrProps-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/SearchModeIdOrProps/target/searchModelIdOrProps-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/searchModelIdOrProps/9.1.10/searchModelIdOrProps-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ searchModelIdOrProps --- [INFO] Installing org/lorainelab/igb/searchModelIdOrProps/9.1.10/searchModelIdOrProps-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ searchModelIdOrProps --- [INFO] Configured Artifact: org.lorainelab.igb:searchModelIdOrProps:9.1.10:jar [INFO] Copying searchModelIdOrProps-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/searchModelIdOrProps-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Advanced Search Tab 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ searchView --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ searchView --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /opt/atlassian/pipelines/agent/build/plugins/SearchView/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/SearchView/src/main/java/com/affymetrix/igb/search/SearchView.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ searchView --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ searchView --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ searchView --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ searchView --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ searchView --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/SearchView/pom.xml to /root/.m2/repository/org/lorainelab/igb/searchView/9.1.10/searchView-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/SearchView/target/searchView-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/searchView/9.1.10/searchView-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ searchView --- [INFO] Installing org/lorainelab/igb/searchView/9.1.10/searchView-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ searchView --- [INFO] Configured Artifact: org.lorainelab.igb:searchView:9.1.10:jar [INFO] Copying searchView-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/searchView-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Sequence Viewer GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ sequenceViewer --- [INFO] Copying 0 resource [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ sequenceViewer --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 11 source files to /opt/atlassian/pipelines/agent/build/plugins/SequenceViewer/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ sequenceViewer --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ sequenceViewer --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ sequenceViewer --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ sequenceViewer --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ sequenceViewer --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/SequenceViewer/pom.xml to /root/.m2/repository/org/lorainelab/igb/sequenceViewer/9.1.10/sequenceViewer-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/SequenceViewer/target/sequenceViewer-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/sequenceViewer/9.1.10/sequenceViewer-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ sequenceViewer --- [INFO] Installing org/lorainelab/igb/sequenceViewer/9.1.10/sequenceViewer-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ sequenceViewer --- [INFO] Configured Artifact: org.lorainelab.igb:sequenceViewer:9.1.10:jar [INFO] Copying sequenceViewer-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/sequenceViewer-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Survey GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ survey --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ survey --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /opt/atlassian/pipelines/agent/build/plugins/Survey/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ survey --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ survey --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ survey --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ survey --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ survey --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Survey/pom.xml to /root/.m2/repository/org/lorainelab/igb/survey/9.1.10/survey-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Survey/target/survey-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/survey/9.1.10/survey-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ survey --- [INFO] Installing org/lorainelab/igb/survey/9.1.10/survey-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ survey --- [INFO] Configured Artifact: org.lorainelab.igb:survey:9.1.10:jar [INFO] Copying survey-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/survey-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Graph thresholding visual analytics 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ thresholding --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ thresholding --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 8 source files to /opt/atlassian/pipelines/agent/build/plugins/Thresholding/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ thresholding --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ thresholding --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ thresholding --- Note: /opt/atlassian/pipelines/agent/build/plugins/Thresholding/src/main/java/com/affymetrix/igb/thresholding/GraphScoreThreshSetter.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ thresholding --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ thresholding --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Thresholding/pom.xml to /root/.m2/repository/org/lorainelab/igb/thresholding/9.1.10/thresholding-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Thresholding/target/thresholding-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/thresholding/9.1.10/thresholding-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ thresholding --- [INFO] Installing org/lorainelab/igb/thresholding/9.1.10/thresholding-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ thresholding --- [INFO] Configured Artifact: org.lorainelab.igb:thresholding:9.1.10:jar [INFO] Copying thresholding-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/thresholding-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Update 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ update --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ update --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /opt/atlassian/pipelines/agent/build/plugins/Update/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ update --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ update --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ update --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ update --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ update --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Update/pom.xml to /root/.m2/repository/org/lorainelab/igb/update/9.1.10/update-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Update/target/update-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/update/9.1.10/update-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ update --- [INFO] Installing org/lorainelab/igb/update/9.1.10/update-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ update --- [INFO] Configured Artifact: org.lorainelab.igb:update:9.1.10:jar [INFO] Copying update-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/update-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - App Manager GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ plugins-manager --- [INFO] Copying 0 resource [INFO] Copying 30 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ plugins-manager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 24 source files to /opt/atlassian/pipelines/agent/build/plugins/plugin-manager/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/plugin-manager/src/main/java/org/lorainelab/igb/plugin/manager/AppManagerFxPanel.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ plugins-manager --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ plugins-manager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/plugin-manager/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ plugins-manager --- [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: 0.023 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] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ plugins-manager --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ plugins-manager --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/plugin-manager/pom.xml to /root/.m2/repository/org/lorainelab/igb/plugins-manager/9.1.10/plugins-manager-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/plugin-manager/target/plugins-manager-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/plugins-manager/9.1.10/plugins-manager-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ plugins-manager --- [INFO] Installing org/lorainelab/igb/plugins-manager/9.1.10/plugins-manager-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ plugins-manager --- [INFO] Configured Artifact: org.lorainelab.igb:plugins-manager:9.1.10:jar [INFO] Copying plugins-manager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/plugins-manager-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Paired-end Read Preprocessor 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ paired-data-preprocessor --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/PairedEndDataPreprocessor/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ paired-data-preprocessor --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/PairedEndDataPreprocessor/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ paired-data-preprocessor --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/PairedEndDataPreprocessor/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ paired-data-preprocessor --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ paired-data-preprocessor --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ paired-data-preprocessor --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ paired-data-preprocessor --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/PairedEndDataPreprocessor/pom.xml to /root/.m2/repository/org/lorainelab/igb/paired-data-preprocessor/9.1.10/paired-data-preprocessor-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/PairedEndDataPreprocessor/target/paired-data-preprocessor-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/paired-data-preprocessor/9.1.10/paired-data-preprocessor-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ paired-data-preprocessor --- [INFO] Installing org/lorainelab/igb/paired-data-preprocessor/9.1.10/paired-data-preprocessor-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ paired-data-preprocessor --- [INFO] Configured Artifact: org.lorainelab.igb:paired-data-preprocessor:9.1.10:jar [INFO] Copying paired-data-preprocessor-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/paired-data-preprocessor-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Save Session Manager 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ session-manager --- [INFO] Copying 0 resource [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ session-manager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/session-manager/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ session-manager --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/session-manager/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ session-manager --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ session-manager --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ session-manager --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ session-manager --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/session-manager/pom.xml to /root/.m2/repository/org/lorainelab/igb/session-manager/9.1.10/session-manager-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/session-manager/target/session-manager-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/session-manager/9.1.10/session-manager-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ session-manager --- [INFO] Installing org/lorainelab/igb/session-manager/9.1.10/session-manager-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ session-manager --- [INFO] Configured Artifact: org.lorainelab.igb:session-manager:9.1.10:jar [INFO] Copying session-manager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/session-manager-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Toolbar Preferences GUI 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ keybinding-registry --- [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ keybinding-registry --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/Keybinding-registry/target/classes Note: /opt/atlassian/pipelines/agent/build/plugins/Keybinding-registry/src/main/java/org/lorainelab/igb/keystrokes/model/KeyStrokeViewTableModel.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ keybinding-registry --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/Keybinding-registry/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ keybinding-registry --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ keybinding-registry --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ keybinding-registry --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ keybinding-registry --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Keybinding-registry/pom.xml to /root/.m2/repository/org/lorainelab/igb/keybinding-registry/9.1.10/keybinding-registry-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/Keybinding-registry/target/keybinding-registry-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/keybinding-registry/9.1.10/keybinding-registry-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ keybinding-registry --- [INFO] Installing org/lorainelab/igb/keybinding-registry/9.1.10/keybinding-registry-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ keybinding-registry --- [INFO] Configured Artifact: org.lorainelab.igb:keybinding-registry:9.1.10:jar [INFO] Copying keybinding-registry-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/keybinding-registry-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Error reporting 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ org.lorainelab.igb.error.reporter.manager --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/org.lorainelab.igb.error.reporter.manager/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ org.lorainelab.igb.error.reporter.manager --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/org.lorainelab.igb.error.reporter.manager/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ org.lorainelab.igb.error.reporter.manager --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/org.lorainelab.igb.error.reporter.manager/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ org.lorainelab.igb.error.reporter.manager --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ org.lorainelab.igb.error.reporter.manager --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ org.lorainelab.igb.error.reporter.manager --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ org.lorainelab.igb.error.reporter.manager --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/org.lorainelab.igb.error.reporter.manager/pom.xml to /root/.m2/repository/org/lorainelab/igb/org.lorainelab.igb.error.reporter.manager/9.1.10/org.lorainelab.igb.error.reporter.manager-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/org.lorainelab.igb.error.reporter.manager/target/org.lorainelab.igb.error.reporter.manager-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/org.lorainelab.igb.error.reporter.manager/9.1.10/org.lorainelab.igb.error.reporter.manager-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ org.lorainelab.igb.error.reporter.manager --- [INFO] Installing org/lorainelab/igb/org.lorainelab.igb.error.reporter.manager/9.1.10/org.lorainelab.igb.error.reporter.manager-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ org.lorainelab.igb.error.reporter.manager --- [INFO] Configured Artifact: org.lorainelab.igb:org.lorainelab.igb.error.reporter.manager:9.1.10:jar [INFO] Copying org.lorainelab.igb.error.reporter.manager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/org.lorainelab.igb.error.reporter.manager-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Feedback 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ feedback --- [INFO] Copying 0 resource [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ feedback --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/feedback/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ feedback --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/feedback/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ feedback --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ feedback --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ feedback --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ feedback --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/feedback/pom.xml to /root/.m2/repository/org/lorainelab/igb/feedback/9.1.10/feedback-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/feedback/target/feedback-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/feedback/9.1.10/feedback-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ feedback --- [INFO] Installing org/lorainelab/igb/feedback/9.1.10/feedback-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ feedback --- [INFO] Configured Artifact: org.lorainelab.igb:feedback:9.1.10:jar [INFO] Copying feedback-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/feedback-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - Narrowpeak data format handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ narrowpeak --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/narrowpeak/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ narrowpeak --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/narrowpeak/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ narrowpeak --- [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ narrowpeak --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ narrowpeak --- [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ narrowpeak --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ narrowpeak --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/narrowpeak/pom.xml to /root/.m2/repository/org/lorainelab/igb/narrowpeak/9.1.10/narrowpeak-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/narrowpeak/target/narrowpeak-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/narrowpeak/9.1.10/narrowpeak-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ narrowpeak --- [INFO] Installing org/lorainelab/igb/narrowpeak/9.1.10/narrowpeak-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ narrowpeak --- [INFO] Configured Artifact: org.lorainelab.igb:narrowpeak:9.1.10:jar [INFO] Copying narrowpeak-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/narrowpeak-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - File Handler - Genotyping Results 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ genotyping --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/GenotypingResults/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ genotyping --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /opt/atlassian/pipelines/agent/build/plugins/GenotypingResults/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ genotyping --- [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ genotyping --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/GenotypingResults/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ genotyping --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest Aug 15, 2022 9:03:47 PM org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest testGetChromosomeList INFO: getChromosomeList Aug 15, 2022 9:03:47 PM org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest testGetLoadChoices INFO: getLoadChoices Aug 15, 2022 9:03:47 PM org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest testParse INFO: parse Aug 15, 2022 9:03:47 PM org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest testParseLineToDataModel INFO: parseLineToDataModel Aug 15, 2022 9:03:47 PM org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest testIsMultiThreadOK INFO: isMultiThreadOK [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 s - in org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ genotyping --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ genotyping --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/GenotypingResults/pom.xml to /root/.m2/repository/org/lorainelab/igb/genotyping/9.1.10/genotyping-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/GenotypingResults/target/genotyping-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/genotyping/9.1.10/genotyping-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ genotyping --- [INFO] Installing org/lorainelab/igb/genotyping/9.1.10/genotyping-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ genotyping --- [INFO] Configured Artifact: org.lorainelab.igb:genotyping:9.1.10:jar [INFO] Copying genotyping-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/genotyping-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - BED file format handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bed --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/bed/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ bed --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/bed/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bed --- [INFO] Copying 4 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ bed --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /opt/atlassian/pipelines/agent/build/plugins/bed/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ bed --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.lorainelab.igb.bed.BedParserTest 21:03:48.136 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 21:03:48.204 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 21:03:48.276 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 21:03:48.325 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 21:03:48.376 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.567 s - in org.lorainelab.igb.bed.BedParserTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ bed --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ bed --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/bed/pom.xml to /root/.m2/repository/org/lorainelab/igb/bed/9.1.10/bed-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/bed/target/bed-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/bed/9.1.10/bed-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ bed --- [INFO] Installing org/lorainelab/igb/bed/9.1.10/bed-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ bed --- [INFO] Configured Artifact: org.lorainelab.igb:bed:9.1.10:jar [INFO] Copying bed-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/bed-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - BAM data format handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bam --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/bam/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ bam --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 5 source files to /opt/atlassian/pipelines/agent/build/plugins/bam/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bam --- [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ bam --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/bam/target/test-classes [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ bam --- [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: 0.276 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: 0.077 s - in org.lorainelab.igb.bam.BAMParserTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ bam --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ bam --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/bam/pom.xml to /root/.m2/repository/org/lorainelab/igb/bam/9.1.10/bam-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/bam/target/bam-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/bam/9.1.10/bam-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ bam --- [INFO] Installing org/lorainelab/igb/bam/9.1.10/bam-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ bam --- [INFO] Configured Artifact: org.lorainelab.igb:bam:9.1.10:jar [INFO] Copying bam-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/bam-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - BAI index visualization handler 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ bai --- [INFO] Copying 0 resource [INFO] Copying 1 resource [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ bai --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 3 source files to /opt/atlassian/pipelines/agent/build/plugins/bai/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ bai --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/bai/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ bai --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ bai --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ bai --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ bai --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/bai/pom.xml to /root/.m2/repository/org/lorainelab/igb/bai/9.1.10/bai-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/bai/target/bai-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/bai/9.1.10/bai-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ bai --- [INFO] Installing org/lorainelab/igb/bai/9.1.10/bai-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ bai --- [INFO] Configured Artifact: org.lorainelab.igb:bai:9.1.10:jar [INFO] Copying bai-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/dynamic/bai-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Plugin - App Store REST API 9.1.10 [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ appstore --- [INFO] Copying 0 resource [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/AppStore/src/main/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ appstore --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/plugins/AppStore/target/classes [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ appstore --- [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/plugins/AppStore/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ appstore --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ appstore --- [INFO] No tests to run. [INFO] [INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ appstore --- [INFO] [INFO] --- maven-install-plugin:3.0.1:install (default-install) @ appstore --- [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/AppStore/pom.xml to /root/.m2/repository/org/lorainelab/igb/appstore/9.1.10/appstore-9.1.10.pom [INFO] Installing /opt/atlassian/pipelines/agent/build/plugins/AppStore/target/appstore-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/appstore/9.1.10/appstore-9.1.10.jar [INFO] [INFO] --- maven-bundle-plugin:3.0.0:install (default-install) @ appstore --- [INFO] Installing org/lorainelab/igb/appstore/9.1.10/appstore-9.1.10.jar [INFO] Writing OBR metadata [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ appstore --- [INFO] Configured Artifact: org.lorainelab.igb:appstore:9.1.10:jar [INFO] Copying appstore-9.1.10.jar to /opt/atlassian/pipelines/agent/build/bundles/appstore-9.1.10.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building IGB Main (run me) 9.1.10 [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/sonatype/install4j/install4j-maven-plugin/1.1.1/install4j-maven-plugin-1.1.1.pom Progress (1): 1.4/4.1 kB Progress (1): 2.7/4.1 kB Progress (1): 4.1 kB Downloaded: https://repo.maven.apache.org/maven2/org/sonatype/install4j/install4j-maven-plugin/1.1.1/install4j-maven-plugin-1.1.1.pom (4.1 kB at 13 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/sonatype/install4j/install4j-support/1.1.1/install4j-support-1.1.1.pom Progress (1): 1.4/13 kB Progress (1): 2.7/13 kB Progress (1): 4.1/13 kB Progress (1): 5.5/13 kB Progress (1): 6.9/13 kB Progress (1): 8.2/13 kB Progress (1): 9.6/13 kB Progress (1): 11/13 kB Progress (1): 12/13 kB Progress (1): 13 kB Downloaded: https://repo.maven.apache.org/maven2/org/sonatype/install4j/install4j-support/1.1.1/install4j-support-1.1.1.pom (13 kB at 403 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/sonatype/buildsupport/public-parent/6/public-parent-6.pom Progress (1): 760 B Downloaded: https://repo.maven.apache.org/maven2/org/sonatype/buildsupport/public-parent/6/public-parent-6.pom (760 B at 27 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/sonatype/buildsupport/buildsupport/6/buildsupport-6.pom Progress (1): 1.4/23 kB Progress (1): 2.7/23 kB Progress (1): 4.1/23 kB Progress (1): 5.5/23 kB Progress (1): 6.9/23 kB Progress (1): 8.2/23 kB Progress (1): 9.6/23 kB Progress (1): 11/23 kB Progress (1): 12/23 kB Progress (1): 14/23 kB Progress (1): 15/23 kB Progress (1): 16/23 kB Progress (1): 17/23 kB Progress (1): 19/23 kB Progress (1): 20/23 kB Progress (1): 21/23 kB Progress (1): 23/23 kB Progress (1): 23 kB Downloaded: https://repo.maven.apache.org/maven2/org/sonatype/buildsupport/buildsupport/6/buildsupport-6.pom (23 kB at 638 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/sonatype/install4j/install4j-maven-plugin/1.1.1/install4j-maven-plugin-1.1.1.jar Progress (1): 1.4/27 kB Progress (1): 2.7/27 kB Progress (1): 4.1/27 kB Progress (1): 5.5/27 kB Progress (1): 6.9/27 kB Progress (1): 8.2/27 kB Progress (1): 9.6/27 kB Progress (1): 11/27 kB Progress (1): 12/27 kB Progress (1): 14/27 kB Progress (1): 15/27 kB Progress (1): 16/27 kB Progress (1): 20/27 kB Progress (1): 24/27 kB Progress (1): 27 kB Downloaded: https://repo.maven.apache.org/maven2/org/sonatype/install4j/install4j-maven-plugin/1.1.1/install4j-maven-plugin-1.1.1.jar (27 kB at 753 kB/s) [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ main --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 0 resource [INFO] Copying 2 resources [INFO] [INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ main --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 2 source files to /opt/atlassian/pipelines/agent/build/main/target/classes [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ main --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /opt/atlassian/pipelines/agent/build/main/src/test/resources [INFO] [INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ main --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.22.2:test (default-test) @ main --- [INFO] No tests to run. [INFO] [INFO] --- maven-jar-plugin:2.5:jar (default-jar) @ main --- [INFO] Building jar: /opt/atlassian/pipelines/agent/build/main/target/main-9.1.10.jar [INFO] [INFO] --- install4j-maven-plugin:1.1.1:install-license (install-license) @ main --- Downloading: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-api/0.9.0.M3/aether-api-0.9.0.M3.pom Progress (1): 1.7 kB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-api/0.9.0.M3/aether-api-0.9.0.M3.pom (1.7 kB at 67 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether/0.9.0.M3/aether-0.9.0.M3.pom Progress (1): 4.1/28 kB Progress (1): 8.2/28 kB Progress (1): 12/28 kB Progress (1): 16/28 kB Progress (1): 20/28 kB Progress (1): 24/28 kB Progress (1): 28/28 kB Progress (1): 28 kB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether/0.9.0.M3/aether-0.9.0.M3.pom (28 kB at 883 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-util/0.9.0.M3/aether-util-0.9.0.M3.pom Progress (1): 2.0 kB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-util/0.9.0.M3/aether-util-0.9.0.M3.pom (2.0 kB at 75 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.1/maven-plugin-annotations-3.1.pom Progress (1): 1.6 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.1/maven-plugin-annotations-3.1.pom (1.6 kB at 65 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-tools/3.1/maven-plugin-tools-3.1.pom Progress (1): 4.1/16 kB Progress (1): 8.2/16 kB Progress (1): 12/16 kB Progress (1): 16/16 kB Progress (1): 16 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-tools/3.1/maven-plugin-tools-3.1.pom (16 kB at 558 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/ant/ant/1.8.4/ant-1.8.4.pom Progress (1): 4.1/9.7 kB Progress (1): 8.2/9.7 kB Progress (1): 9.7 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/ant/ant/1.8.4/ant-1.8.4.pom (9.7 kB at 186 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/ant/ant-parent/1.8.4/ant-parent-1.8.4.pom Progress (1): 4.1/4.6 kB Progress (1): 4.6 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/ant/ant-parent/1.8.4/ant-parent-1.8.4.pom (4.6 kB at 169 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/ant/ant-launcher/1.8.4/ant-launcher-1.8.4.pom Progress (1): 2.4 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/ant/ant-launcher/1.8.4/ant-launcher-1.8.4.pom (2.4 kB at 91 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/2.2.1/maven-reporting-api-2.2.1.jar Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.jar Downloading: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-api/0.9.0.M3/aether-api-0.9.0.M3.jar Downloading: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-util/0.9.0.M3/aether-util-0.9.0.M3.jar Downloading: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.1/maven-plugin-annotations-3.1.jar Progress (1): 4.1/13 kB Progress (1): 8.2/13 kB Progress (1): 12/13 kB Progress (1): 13 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.jar (13 kB at 388 kB/s) Downloading: https://repo.maven.apache.org/maven2/org/apache/ant/ant/1.8.4/ant-1.8.4.jar Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB Progress (1): 0/1.9 MB 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4.1/135 kB | 5.5/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 8.2/9.8 kB | 5.5/135 kB | 5.5/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.6/9.8 kB | 5.5/135 kB | 5.5/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.6/9.8 kB | 5.5/135 kB | 6.9/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.6/9.8 kB | 5.5/135 kB | 6.9/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.6/9.8 kB | 5.5/135 kB | 8.2/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.6/9.8 kB | 5.5/135 kB | 8.2/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 5.5/135 kB | 8.2/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 6.9/135 kB | 8.2/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 6.9/135 kB | 8.2/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 6.9/135 kB | 9.6/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 8.2/135 kB | 9.6/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 8.2/135 kB | 11/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 8.2/135 kB | 11/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 9.6/135 kB | 11/142 kB 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Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 15/135 kB | 20/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 15/135 kB | 20/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 15/135 kB | 21/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 16/135 kB | 21/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 16/135 kB | 23/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 16/135 kB | 23/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 17/135 kB | 23/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 17/135 kB | 24/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 19/135 kB | 24/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 19/135 kB | 24/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 19/135 kB | 25/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 19/135 kB | 25/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 20/135 kB | 25/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 20/135 kB | 25/142 kB Progress (5): 0.1/1.9 MB | 14 kB | 9.8 kB | 20/135 kB | 27/142 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.1/maven-plugin-annotations-3.1.jar (14 kB at 178 kB/s) Progress (4): 0.1/1.9 MB | 9.8 kB | 20/135 kB | 28/142 kB Progress (4): 0.1/1.9 MB | 9.8 kB | 20/135 kB | 28/142 kB Progress (4): 0.1/1.9 MB | 9.8 kB | 21/135 kB | 28/142 kB Progress (4): 0.1/1.9 MB | 9.8 kB | 21/135 kB | 30/142 kB Downloading: https://repo.maven.apache.org/maven2/org/apache/ant/ant-launcher/1.8.4/ant-launcher-1.8.4.jar Progress (4): 0.1/1.9 MB | 9.8 kB | 21/135 kB | 31/142 kB Progress (4): 0.1/1.9 MB | 9.8 kB | 23/135 kB | 31/142 kB Progress (4): 0.1/1.9 MB | 9.8 kB | 23/135 kB | 32/142 kB Progress (4): 0.2/1.9 MB | 9.8 kB | 23/135 kB | 32/142 kB Progress (4): 0.2/1.9 MB | 9.8 kB | 24/135 kB | 32/142 kB Progress (4): 0.2/1.9 MB | 9.8 kB | 24/135 kB | 34/142 kB Progress (4): 0.2/1.9 MB | 9.8 kB | 24/135 kB | 34/142 kB Progress (4): 0.2/1.9 MB | 9.8 kB | 24/135 kB | 35/142 kB Progress (4): 0.2/1.9 MB | 9.8 kB | 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(3): 0.2/1.9 MB | 40/135 kB | 73/142 kB Progress (3): 0.2/1.9 MB | 40/135 kB | 73/142 kB Progress (3): 0.2/1.9 MB | 40/135 kB | 77/142 kB Progress (3): 0.2/1.9 MB | 42/135 kB | 77/142 kB Progress (3): 0.2/1.9 MB | 42/135 kB | 81/142 kB Progress (3): 0.2/1.9 MB | 42/135 kB | 81/142 kB Progress (3): 0.2/1.9 MB | 43/135 kB | 81/142 kB Progress (3): 0.2/1.9 MB | 43/135 kB | 81/142 kB Progress (3): 0.2/1.9 MB | 43/135 kB | 85/142 kB Progress (3): 0.2/1.9 MB | 43/135 kB | 85/142 kB Progress (3): 0.2/1.9 MB | 45/135 kB | 85/142 kB Progress (3): 0.2/1.9 MB | 45/135 kB | 85/142 kB Progress (3): 0.2/1.9 MB | 45/135 kB | 90/142 kB Progress (3): 0.2/1.9 MB | 46/135 kB | 90/142 kB Progress (3): 0.2/1.9 MB | 46/135 kB | 94/142 kB Progress (3): 0.2/1.9 MB | 46/135 kB | 98/142 kB Progress (3): 0.2/1.9 MB | 47/135 kB | 98/142 kB Progress (3): 0.2/1.9 MB | 47/135 kB | 98/142 kB Progress (3): 0.2/1.9 MB | 47/135 kB | 98/142 kB Progress (3): 0.2/1.9 MB | 47/135 kB | 102/142 kB Progress (3): 0.2/1.9 MB | 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Progress (4): 0.2/1.9 MB | 65/135 kB | 135/142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 135/142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 139/142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 139/142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 1.4/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 65/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 69/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 73/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 77/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 81/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 85/135 kB | 142 kB | 2.7/18 kB Progress (4): 0.3/1.9 MB | 85/135 kB | 142 kB | 4.1/18 kB Progress (4): 0.3/1.9 MB | 90/135 kB | 142 kB | 4.1/18 kB Progress (4): 0.3/1.9 MB | 90/135 kB | 142 kB | 4.1/18 kB Progress (4): 0.3/1.9 MB | 94/135 kB | 142 kB | 4.1/18 kB Progress (4): 0.3/1.9 MB | 94/135 kB | 142 kB | 5.5/18 kB Progress (4): 0.3/1.9 MB | 94/135 kB | 142 kB | 5.5/18 kB Progress (4): 0.3/1.9 MB | 98/135 kB | 142 kB | 5.5/18 kB Progress (4): 0.3/1.9 MB | 98/135 kB | 142 kB | 5.5/18 kB Progress (4): 0.3/1.9 MB | 98/135 kB | 142 kB | 6.9/18 kB Progress (4): 0.3/1.9 MB | 98/135 kB | 142 kB | 6.9/18 kB Progress (4): 0.3/1.9 MB | 102/135 kB | 142 kB | 6.9/18 kB Progress (4): 0.3/1.9 MB | 102/135 kB | 142 kB | 8.2/18 kB Progress (4): 0.3/1.9 MB | 106/135 kB | 142 kB | 8.2/18 kB Progress (4): 0.3/1.9 MB | 106/135 kB | 142 kB | 8.2/18 kB Progress (4): 0.3/1.9 MB | 106/135 kB | 142 kB | 9.6/18 kB Progress (4): 0.3/1.9 MB | 106/135 kB | 142 kB | 9.6/18 kB Progress (4): 0.3/1.9 MB | 110/135 kB | 142 kB | 9.6/18 kB Progress (4): 0.3/1.9 MB | 110/135 kB | 142 kB | 9.6/18 kB Progress (4): 0.3/1.9 MB | 110/135 kB | 142 kB | 11/18 kB Progress (4): 0.3/1.9 MB | 110/135 kB | 142 kB | 11/18 kB Progress (4): 0.3/1.9 MB | 114/135 kB | 142 kB | 11/18 kB Progress (4): 0.3/1.9 MB | 114/135 kB | 142 kB | 12/18 kB Progress (4): 0.3/1.9 MB | 114/135 kB | 142 kB | 12/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 12/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 14/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 14/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 14/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 15/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 16/18 kB Progress (4): 0.4/1.9 MB | 114/135 kB | 142 kB | 16/18 kB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-util/0.9.0.M3/aether-util-0.9.0.M3.jar (142 kB at 1.3 MB/s) Progress (3): 0.4/1.9 MB | 114/135 kB | 16/18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 17/18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 17/18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 17/18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 114/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 118/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 122/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 126/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 126/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 131/135 kB | 18 kB Progress (3): 0.4/1.9 MB | 131/135 kB | 18 kB 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MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.5/1.9 MB | 135 kB | 18 kB Progress (3): 0.6/1.9 MB | 135 kB | 18 kB Progress (3): 0.6/1.9 MB | 135 kB | 18 kB Progress (3): 0.6/1.9 MB | 135 kB | 18 kB Downloaded: https://repo.maven.apache.org/maven2/org/apache/ant/ant-launcher/1.8.4/ant-launcher-1.8.4.jar (18 kB at 152 kB/s) Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.6/1.9 MB | 135 kB Progress (2): 0.7/1.9 MB | 135 kB Progress (2): 0.7/1.9 MB | 135 kB Downloaded: https://repo.maven.apache.org/maven2/org/eclipse/aether/aether-api/0.9.0.M3/aether-api-0.9.0.M3.jar (135 kB at 1.1 MB/s) Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 MB Progress (1): 0.7/1.9 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[INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @ main --- [INFO] Installing /opt/atlassian/pipelines/agent/build/main/target/main-9.1.10.jar to /root/.m2/repository/org/lorainelab/igb/main/9.1.10/main-9.1.10.jar [INFO] Installing /opt/atlassian/pipelines/agent/build/main/pom.xml to /root/.m2/repository/org/lorainelab/igb/main/9.1.10/main-9.1.10.pom [INFO] [INFO] --- maven-dependency-plugin:2.9:copy-dependencies (copy) @ main --- [INFO] Copying commons-lang3-3.4.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/commons-lang3-3.4.jar [INFO] Copying affymetrix-common-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/affymetrix-common-9.1.10.jar [INFO] Copying shared-lib-wrapper-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/shared-lib-wrapper-9.1.10.jar [INFO] Copying org.apache.felix.webconsole-4.3.12.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.webconsole-4.3.12.jar [INFO] Copying context-menu-service-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/context-menu-service-9.1.10.jar [INFO] Copying keybinding-registry-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/keybinding-registry-9.1.10.jar [INFO] Copying org.apache.felix.eventadmin-1.5.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.eventadmin-1.5.0.jar [INFO] Copying cache-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/cache-9.1.10.jar [INFO] Copying session-manager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/session-manager-9.1.10.jar [INFO] Copying org.apache.felix.http.jetty-4.0.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.http.jetty-4.0.10.jar [INFO] Copying image-exporter-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/image-exporter-9.1.10.jar [INFO] Copying commons-jexl-2.1.1.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/commons-jexl-2.1.1.jar [INFO] Copying heatmap-editor-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/heatmap-editor-9.1.10.jar [INFO] Copying org.apache.felix.dependencymanager-3.2.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.dependencymanager-3.2.0.jar [INFO] Copying igb-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/igb-9.1.10.jar [INFO] Copying igb-services-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/igb-services-9.1.10.jar [INFO] Copying bigBedHandler-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/bigBedHandler-9.1.10.jar [INFO] Copying logging-config-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/logging-config-9.1.10.jar [INFO] Copying quickload-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/quickload-9.1.10.jar [INFO] Copying xz-1.5.jar to 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org.osgi.service.remoteserviceadmin-1.1.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.osgi.service.remoteserviceadmin-1.1.0.jar [INFO] Copying org.lorainelab.igb.error.reporter.manager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.lorainelab.igb.error.reporter.manager-9.1.10.jar [INFO] Copying igbScript-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/igbScript-9.1.10.jar [INFO] Copying genotyping-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/genotyping-9.1.10.jar [INFO] Copying commons-csv-1.2.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/commons-csv-1.2.jar [INFO] Copying plugins-manager-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/plugins-manager-9.1.10.jar [INFO] Copying org.lorainelab.igb.remote.services.topology.manager-1.0.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.lorainelab.igb.remote.services.topology.manager-1.0.0.jar [INFO] Copying commons-logging-1.2.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/commons-logging-1.2.jar [INFO] Copying track-operations-panel-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/track-operations-panel-9.1.10.jar [INFO] Copying guava-16.0.1.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/guava-16.0.1.jar [INFO] Copying bigwig-2.0.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/bigwig-2.0.0.jar [INFO] Copying window-service-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/window-service-9.1.10.jar [INFO] Copying jide-ultimate-3.5.15.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/jide-ultimate-3.5.15.jar [INFO] Copying logback-classic-1.1.2.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/logback-classic-1.1.2.jar [INFO] Copying commons-codec-1.6.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/commons-codec-1.6.jar [INFO] Copying external-sort-9.1.10.jar to 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/opt/atlassian/pipelines/agent/build/main/target/lib/bam-9.1.10.jar [INFO] Copying org.apache.felix.main-5.2.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.main-5.2.0.jar [INFO] Copying jackson-core-2.3.5.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/jackson-core-2.3.5.jar [INFO] Copying org.apache.felix.http.bundle-2.3.2.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.http.bundle-2.3.2.jar [INFO] Copying externalView-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/externalView-9.1.10.jar [INFO] Copying apollo-library-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/apollo-library-9.1.10.jar [INFO] Copying synonym-lookup-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/synonym-lookup-9.1.10.jar [INFO] Copying bookmark-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/bookmark-9.1.10.jar [INFO] Copying propertyView-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/propertyView-9.1.10.jar [INFO] Copying survey-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/survey-9.1.10.jar [INFO] Copying org.apache.felix.http.servlet-api-1.1.2.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.http.servlet-api-1.1.2.jar [INFO] Copying igb-javafx-util-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/igb-javafx-util-9.1.10.jar [INFO] Copying org.apache.felix.bundlerepository-2.0.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.bundlerepository-2.0.10.jar [INFO] Copying bai-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/bai-9.1.10.jar [INFO] Copying org.lorainelab.igb.menu.api-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.lorainelab.igb.menu.api-9.1.10.jar [INFO] Copying sequenceViewer-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/sequenceViewer-9.1.10.jar [INFO] Copying feedback-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/feedback-9.1.10.jar [INFO] Copying bed-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/bed-9.1.10.jar [INFO] Copying org.lorainelab.igb.error.reporter.api-1.0.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.lorainelab.igb.error.reporter.api-1.0.0.jar [INFO] Copying console-tab-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/console-tab-9.1.10.jar [INFO] Copying org.apache.felix.scr-1.8.2.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.scr-1.8.2.jar [INFO] Copying org.apache.felix.configadmin-1.8.8.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.apache.felix.configadmin-1.8.8.jar [INFO] Copying update-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/update-9.1.10.jar [INFO] Copying igb-preferences-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/igb-preferences-9.1.10.jar [INFO] Copying commons-compress-1.5.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/commons-compress-1.5.jar [INFO] Copying slf4j-api-1.7.7.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/slf4j-api-1.7.7.jar [INFO] Copying org.osgi.compendium-5.0.0.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/org.osgi.compendium-5.0.0.jar [INFO] Copying genometry-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/genometry-9.1.10.jar [INFO] Copying igb-genoviz-extensions-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/igb-genoviz-extensions-9.1.10.jar [INFO] [INFO] --- maven-dependency-plugin:2.9:copy (copy) @ main --- [INFO] Configured Artifact: org.lorainelab.igb:main:9.1.10:jar [INFO] Copying main-9.1.10.jar to /opt/atlassian/pipelines/agent/build/main/target/lib/main-9.1.10.jar [INFO] [INFO] --- maven-antrun-plugin:1.7:run (buildExecutableJar) @ main --- [INFO] Executing tasks main: [jar] Building jar: /opt/atlassian/pipelines/agent/build/igb_exe.jar [INFO] Executed tasks [INFO] [INFO] --- install4j-maven-plugin:1.1.1:compile (compile-installers) @ main --- [INFO] install4j version 9.0.7 (build 9184), built on 2022-05-23 [INFO] Registered to [INFO] [INFO] Loading config file /opt/atlassian/pipelines/agent/build/distribution/install4jv9.install4j------------------------------------------------------------------------------ [INFO] The private key is encrypted. To avoid manual intervention, set the [INFO] "--win-keystore-password" command line option or the [INFO] install4j: compilation failed. Reason: null [INFO] "winKeystorePassword" gradle task property or ant task attribute. [INFO] ------------------------------------------------------------------------------ [INFO] Enter the password for the Windows key store: [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] IGB Project ........................................ SUCCESS [ 0.142 s] [INFO] Core - Heatmap Editor .............................. SUCCESS [ 3.058 s] [INFO] Core - Affymetrix Common ........................... SUCCESS [ 3.573 s] [INFO] Plugin - Sorting API and Impl ...................... SUCCESS [ 1.343 s] [INFO] Plugin - Data caching API .......................... SUCCESS [ 0.121 s] [INFO] Core - Synonym Lookup .............................. SUCCESS [ 0.961 s] [INFO] Core - Genometry (Data Models) ..................... SUCCESS [ 7.389 s] [INFO] Core - Preferences ................................. SUCCESS [ 1.067 s] [INFO] Core - IGB Swing Extensions ........................ SUCCESS [ 0.538 s] [INFO] Core - Genoviz Extensions .......................... SUCCESS [ 0.237 s] [INFO] Core - IGB Services API ............................ SUCCESS [ 0.226 s] [INFO] Core - Frame Manager ............................... SUCCESS [ 0.176 s] [INFO] Core - Window Service .............................. SUCCESS [ 0.288 s] [INFO] Core - JavaFX Utilities ............................ SUCCESS [ 0.132 s] [INFO] Core - Menu API .................................... SUCCESS [ 0.160 s] [INFO] Core - Context Menu Service ........................ SUCCESS [ 0.166 s] [INFO] Core - IGB ......................................... SUCCESS [ 4.847 s] [INFO] Core - Bundle wrapper, deployer .................... SUCCESS [ 2.625 s] [INFO] Core - Logging Config .............................. SUCCESS [ 0.069 s] [INFO] Core - Web Links ................................... SUCCESS [ 0.436 s] [INFO] Plugin - Data caching GUI .......................... SUCCESS [ 0.984 s] [INFO] Core - Quickload (data source) ..................... SUCCESS [ 1.243 s] [INFO] Core - DAS (data source) ........................... SUCCESS [ 1.876 s] [INFO] Plugin - Apollo Library ............................ SUCCESS [ 0.144 s] [INFO] Plugin - Track Operations API, GUI ................. SUCCESS [ 0.280 s] [INFO] Plugin - Annotation Tab ............................ SUCCESS [ 0.248 s] [INFO] Plugin - Console Tab ............................... SUCCESS [ 0.206 s] [INFO] Plugin - Bigbed data format handler ................ SUCCESS [ 0.139 s] [INFO] Plugin - Bigwig data format handler ................ SUCCESS [ 0.152 s] [INFO] Plugin - Bookmarks and REST API .................... SUCCESS [ 1.193 s] [INFO] Plugin - External View ............................. SUCCESS [ 3.900 s] [INFO] Plugin - Graph Tab ................................. SUCCESS [ 0.262 s] [INFO] Plugin - Save Image GUI ............................ SUCCESS [ 0.922 s] [INFO] Plugin - Script handler ............................ SUCCESS [ 0.183 s] [INFO] Plugin - Keyword Search ............................ SUCCESS [ 0.107 s] [INFO] Plugin - NCBI Blast ................................ SUCCESS [ 2.984 s] [INFO] Plugin - Selection Info tab ........................ SUCCESS [ 0.228 s] [INFO] Plugin - Restriction Sites tab ..................... SUCCESS [ 0.220 s] [INFO] Plugin - Search Id or Props ........................ SUCCESS [ 0.134 s] [INFO] Plugin - Advanced Search Tab ....................... SUCCESS [ 0.322 s] [INFO] Plugin - Sequence Viewer GUI ....................... SUCCESS [ 0.305 s] [INFO] Plugin - Survey GUI ................................ SUCCESS [ 0.146 s] [INFO] Plugin - Graph thresholding visual analytics ....... SUCCESS [ 0.258 s] [INFO] Plugin - Update .................................... SUCCESS [ 0.142 s] [INFO] Plugin - App Manager GUI ........................... SUCCESS [ 1.475 s] [INFO] Plugin - Paired-end Read Preprocessor .............. SUCCESS [ 0.113 s] [INFO] Plugin - Save Session Manager ...................... SUCCESS [ 0.180 s] [INFO] Plugin - Toolbar Preferences GUI ................... SUCCESS [ 0.340 s] [INFO] Plugin - Error reporting ........................... SUCCESS [ 0.175 s] [INFO] Plugin - Feedback .................................. SUCCESS [ 0.166 s] [INFO] Plugin - Narrowpeak data format handler ............ SUCCESS [ 0.144 s] [INFO] Plugin - File Handler - Genotyping Results ........ SUCCESS [ 1.065 s] [INFO] Plugin - BED file format handler ................... SUCCESS [ 1.317 s] [INFO] Plugin - BAM data format handler ................... SUCCESS [ 1.164 s] [INFO] Plugin - BAI index visualization handler ........... SUCCESS [ 0.189 s] [INFO] Plugin - App Store REST API ........................ SUCCESS [ 0.119 s] [INFO] IGB Main (run me) .................................. FAILURE [ 14.126 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:05 min [INFO] Finished at: 2022-08-15T21:04:04Z [INFO] Final Memory: 127M/421M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.sonatype.install4j:install4j-maven-plugin:1.1.1:compile (compile-installers) on project main: null returned: 1 -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :main Skipping cache upload for failed step Searching for test report files in directories named [test-results, failsafe-reports, test-reports, TestResults, surefire-reports] down to a depth of 4 Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/cache/target/surefire-reports/TEST-com.lorainelab.cache.disk.RemoteFileCacheServiceTest.xml Located test suite containing 8 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/ExternalView/target/surefire-reports/TEST-com.affymetrix.igb.external.LoaderTest.xml Located test suite containing 4 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/ExternalView/target/surefire-reports/TEST-com.affymetrix.igb.external.EndPointTest.xml Located test suite containing 5 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/external-sort/target/surefire-reports/TEST-org.lorainelab.igb.externalsort.ExternalSortTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/GenotypingResults/target/surefire-reports/TEST-org.lorainelab.igb.genotyping.TwentyThreeAndMeSymLoaderTest.xml Located test suite containing 5 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/bam/target/surefire-reports/TEST-org.lorainelab.igb.bam.SAMParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/bam/target/surefire-reports/TEST-org.lorainelab.igb.bam.BAMParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/NCBIBlast/target/surefire-reports/TEST-apollo.analysis.RemoteBlastNCBITest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/bed/target/surefire-reports/TEST-org.lorainelab.igb.bed.BedParserTest.xml Located test suite containing 11 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/plugin-manager/target/surefire-reports/TEST-org.lorainelab.igb.plugin.manager.PluginManagerFxPanelTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/plugins/Bookmark/target/surefire-reports/TEST-com.affymetrix.igb.bookmarks.BookMarkTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/igb-preferences/target/surefire-reports/TEST-com.lorainelab.igb.preferences.IgbPreferencesParseTest.xml Located test suite containing 5 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/das/target/surefire-reports/TEST-com.lorainelab.das.DASFeatureParserTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/das/target/surefire-reports/TEST-com.lorainelab.das.DasServerInfoTest.xml Located test suite containing 5 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/das/target/surefire-reports/TEST-com.lorainelab.das.DasDataProviderTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/synonym-lookup/target/surefire-reports/TEST-org.lorainelab.igb.synonymlookup.test.SynonymLookupTest.xml Located test suite containing 5 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.UseqParserTest.xml Located test suite containing 4 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.BgrParserTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.GFFParserTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.util.IgbStringUtilsTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.CntParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.NibbleResiduesParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.GFF3SymTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.ScoredIntervalParserTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.util.SeqUtilsTest.xml Located test suite containing 8 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.FastaParserTest.xml Located test suite containing 8 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.TrackLineParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.NibbleFileParserTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.PSLParserTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.NibbleBioSeqTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.BioSeqTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.CytobandParserTest.xml Located test suite containing 4 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.TwoBitParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.comparator.SeqSymIdComparatorTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.GFF3ParserTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.TwoBitNewTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.SamRecordFlagTest.xml Located test suite containing 8 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.BpsParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.Bprobe1ParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.BrsParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.WiggleParserTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.BarParserTest.xml Located test suite containing 3 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.GrParserTest.xml Located test suite containing 4 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/genometry/target/surefire-reports/TEST-com.affymetrix.genometry.parsers.graph.SgrParserTest.xml Located test suite containing 4 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/quickload/target/surefire-reports/TEST-org.lorainelab.igb.quickload.utils.QuickloadUtilsTest.xml Located test suite containing 2 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/quickload/target/surefire-reports/TEST-org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest.xml Located test suite containing 5 tests, with 0 failures and 0 errors. Found matching test report file /opt/atlassian/pipelines/agent/build/core/quickload/target/surefire-reports/TEST-org.lorainelab.igb.quickload.utils.AnnotsParserTest.xml Located test suite containing 1 tests, with 0 failures and 0 errors. Finished scanning for test reports. Found 47 test report files. Merged test suites, total number tests is 148, with 0 failures and 0 errors. Uploading test results Finished uploading test results.