+ 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 13:26:10.926 [main] DEBUG c.g.c.e.ExternalMergeSort - Temp file count: 1 13:26:10.944 [main] INFO o.l.i.externalsort.ExternalSortTest - 33.78 ms [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 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: 0.175 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: 0.043 s - in com.affymetrix.genometry.NibbleBioSeqTest [INFO] Running com.affymetrix.genometry.GFF3SymTest [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 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: 0.001 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 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: 1.083 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: 0.002 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: 0.032 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: 0.03 s - in com.affymetrix.genometry.parsers.graph.BgrParserTest [INFO] Running com.affymetrix.genometry.parsers.graph.BarParserTest Aug 16, 2022 1:26:17 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: 0.035 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: 0.109 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: 0.162 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: 0.024 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: 0.005 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: 0.121 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: 0.009 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: 0.013 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: 0.012 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 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 14 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 3 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 4 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 3 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 26 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 20 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 10 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 9 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 36 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 2 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 1 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 2 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 15 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 27 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 in NibbleIterator.stringToNibbles(), start >= end NOT YET IMPLEMENTED Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse in NibbleIterator.stringToNibbles(), start >= end NOT YET IMPLEMENTED INFO: Chromosome: chrQ : residues: 0 Aug 16, 2022 1:26:18 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse INFO: Chromosome: chrQ : residues: 37 [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 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: 0.219 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: 0.018 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: 0.191 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: 0.008 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: 0.013 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: 0.099 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: 0.004 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: 0.349 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.services.registry, com.affymetrix.igb.view], [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: 0.042 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: 0.207 s - in org.lorainelab.igb.quickload.utils.AnnotsParserTest [INFO] Running org.lorainelab.igb.quickload.utils.QuickloadDataProviderTest Aug 16, 2022 1:26:34 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. 13:26:34.779 [main] INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server file:/opt/atlassian/pipelines/agent/build/core/quickload/target/test-classes/quickload/ 13:26:34.790 [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 13:26:34.790 [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: 0.138 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: 0.009 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: 125.351 s - in com.lorainelab.das.DasDataProviderTest [INFO] Running com.lorainelab.das.DasServerInfoTest [WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.001 s - in com.lorainelab.das.DasServerInfoTest [INFO] Running com.lorainelab.das.DASFeatureParserTest [INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.17 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: 0.093 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 [ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 124.926 s <<< FAILURE! - in com.affymetrix.igb.external.EndPointTest [ERROR] com.affymetrix.igb.external.EndPointTest Time elapsed: 124.926 s <<< FAILURE! junit.framework.AssertionFailedError: UCSC JSON API endpoint should provide content. at com.affymetrix.igb.external.EndPointTest.beforeAllTestMethods(EndPointTest.java:50) [INFO] Running com.affymetrix.igb.external.LoaderTest 13:30:50.185 INFO c.a.igb.external.ENSEMBLoader - Made URL string: {0} [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.983 s - in com.affymetrix.igb.external.LoaderTest [INFO] [INFO] Results: [INFO] [ERROR] Failures: [ERROR] EndPointTest.beforeAllTestMethods:50 UCSC JSON API endpoint should provide content. [INFO] [ERROR] Tests run: 5, Failures: 1, Errors: 0, Skipped: 1 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] IGB Project ........................................ SUCCESS [ 0.114 s] [INFO] Core - Heatmap Editor .............................. SUCCESS [ 3.453 s] [INFO] Core - Affymetrix Common ........................... SUCCESS [ 4.317 s] [INFO] Plugin - Sorting API and Impl ...................... SUCCESS [ 1.490 s] [INFO] Plugin - Data caching API .......................... SUCCESS [ 0.131 s] [INFO] Core - Synonym Lookup .............................. SUCCESS [ 1.064 s] [INFO] Core - Genometry (Data Models) ..................... SUCCESS [ 7.988 s] [INFO] Core - Preferences ................................. SUCCESS [ 1.155 s] [INFO] Core - IGB Swing Extensions ........................ SUCCESS [ 0.602 s] [INFO] Core - Genoviz Extensions .......................... SUCCESS [ 0.252 s] [INFO] Core - IGB Services API ............................ SUCCESS [ 0.268 s] [INFO] Core - Frame Manager ............................... SUCCESS [ 0.163 s] [INFO] Core - Window Service .............................. SUCCESS [ 0.311 s] [INFO] Core - JavaFX Utilities ............................ SUCCESS [ 0.195 s] [INFO] Core - Menu API .................................... SUCCESS [ 0.157 s] [INFO] Core - Context Menu Service ........................ SUCCESS [ 0.144 s] [INFO] Core - IGB ......................................... SUCCESS [ 5.932 s] [INFO] Core - Bundle wrapper, deployer .................... SUCCESS [ 2.688 s] [INFO] Core - Logging Config .............................. SUCCESS [ 0.094 s] [INFO] Core - Web Links ................................... SUCCESS [ 0.411 s] [INFO] Plugin - Data caching GUI .......................... SUCCESS [ 1.015 s] [INFO] Core - Quickload (data source) ..................... SUCCESS [ 1.298 s] [INFO] Core - DAS (data source) ........................... SUCCESS [02:06 min] [INFO] Plugin - Apollo Library ............................ SUCCESS [ 0.195 s] [INFO] Plugin - Track Operations API, GUI ................. SUCCESS [ 0.366 s] [INFO] Plugin - Annotation Tab ............................ SUCCESS [ 0.305 s] [INFO] Plugin - Console Tab ............................... SUCCESS [ 0.272 s] [INFO] Plugin - Bigbed data format handler ................ SUCCESS [ 0.161 s] [INFO] Plugin - Bigwig data format handler ................ SUCCESS [ 0.192 s] [INFO] Plugin - Bookmarks and REST API .................... SUCCESS [ 1.318 s] [INFO] Plugin - External View ............................. FAILURE [02:07 min] [INFO] Plugin - Graph Tab ................................. SKIPPED [INFO] Plugin - Save Image GUI ............................ SKIPPED [INFO] Plugin - Script handler ............................ SKIPPED [INFO] Plugin - Keyword Search ............................ SKIPPED [INFO] Plugin - NCBI Blast ................................ SKIPPED [INFO] Plugin - Selection Info tab ........................ SKIPPED [INFO] Plugin - Restriction Sites tab ..................... SKIPPED [INFO] Plugin - Search Id or Props ........................ SKIPPED [INFO] Plugin - Advanced Search Tab ....................... SKIPPED [INFO] Plugin - Sequence Viewer GUI ....................... SKIPPED [INFO] Plugin - Survey GUI ................................ SKIPPED [INFO] Plugin - Graph thresholding visual analytics ....... SKIPPED [INFO] Plugin - Update .................................... SKIPPED [INFO] Plugin - App Manager GUI ........................... SKIPPED [INFO] Plugin - Paired-end Read Preprocessor .............. SKIPPED [INFO] Plugin - Save Session Manager ...................... SKIPPED [INFO] Plugin - Toolbar Preferences GUI ................... SKIPPED [INFO] Plugin - Error reporting ........................... SKIPPED [INFO] Plugin - Feedback .................................. SKIPPED [INFO] Plugin - Narrowpeak data format handler ............ SKIPPED [INFO] Plugin - File Handler - Genotyping Results ........ SKIPPED [INFO] Plugin - BED file format handler ................... SKIPPED [INFO] Plugin - BAM data format handler ................... SKIPPED [INFO] Plugin - BAI index visualization handler ........... SKIPPED [INFO] Plugin - App Store REST API ........................ SKIPPED [INFO] IGB Main (run me) .................................. SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 04:51 min [INFO] Finished at: 2022-08-16T13:30:52Z [INFO] Final Memory: 83M/435M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.2:test (default-test) on project externalView: There are test failures. [ERROR] [ERROR] Please refer to /opt/atlassian/pipelines/agent/build/plugins/ExternalView/target/surefire-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream. [ERROR] -> [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/MojoFailureException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn -rf :externalView 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 1 tests, with 1 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/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 41 test report files. Merged test suites, total number tests is 123, with 1 failures and 0 errors. Uploading test results Finished uploading test results.