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Started by upstream project "BIOFORMATS-test-repo" build number 297 originally caused by: Started by upstream project "Trigger" build number 319 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins14800885565734151313.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47025_merge_ci -v /uod/idr/repos/curated/imspector:/data -v /uod/idr-scratch/merge-ci/curated/imspector:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml compile-tests: [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [resolver:resolve] Resolving artifacts [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-mdbtools/5.3.4-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/metakit/5.3.8-SNAPSHOT/maven-metadata.xml [resolver:resolve] Downloading https://maven.imagej.net/content/groups/public/org/openmicroscopy/ome-poi/5.3.10-SNAPSHOT/maven-metadata.xml [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 03:50:04,670 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:50:04,672 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:50:04,672 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:50:04,673 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:50:04,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:50:04,674 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:50:04,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:50:04,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:50:04,674 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:50:04,675 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:50:04,675 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:50:04,675 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:50:04,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:50:04,940 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:50:04,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:50:04,968 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:50:04,976 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:50:04,976 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:50:04,976 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:50:04,977 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:50:04,977 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:50:04,978 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:50:04,978 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 304 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-24 03:50:04,987] [main] java.version = 1.8.0_342 [testng] 03:50:04,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:50:04,991 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:05,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-24_03-50-05.log] [testng] 03:50:05,035 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-24 03:50:05,037] [main] testng.directory = /data [testng] [2024-12-24 03:50:05,037] [main] testng.configDirectory = /config [testng] [2024-12-24 03:50:05,049] [main] testng.multiplier = 1.0 [testng] [2024-12-24 03:50:05,049] [main] testng.in-memory = false [testng] [2024-12-24 03:50:05,049] [main] testng.allow-missing = false [testng] [2024-12-24 03:50:05,049] [main] user.language = en [testng] [2024-12-24 03:50:05,050] [main] user.country = ${user.country} [testng] [2024-12-24 03:50:05,050] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-24 03:50:21,841] [main] ---------------------------------------- [testng] [2024-12-24 03:50:21,841] [main] Total files: 29 [testng] [2024-12-24 03:50:21,841] [main] Scan time: 16.791 s (579 ms/file) [testng] [2024-12-24 03:50:21,842] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-24 03:50:45,541] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] 03:50:45,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:50:45,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:45,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-24_03-50-45.log] [testng] 03:50:45,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f17b91c - End of configuration. [testng] [2024-12-24 03:50:46,099] [pool-1-thread-12] Initializing /data/qa-7936/01 - working.msr: [testng] 03:50:46,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:50:46,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:46,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-24_03-50-46.log] [testng] 03:50:46,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39104950 - End of configuration. [testng] [2024-12-24 03:50:46,639] [pool-1-thread-11] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 03:50:46,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:50:46,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:46,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-24_03-50-46.log] [testng] 03:50:46,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6508e360 - End of configuration. [testng] [2024-12-24 03:50:47,714] [pool-1-thread-10] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 03:50:47,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:50:47,714 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:47,715 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-24_03-50-47.log] [testng] 03:50:47,715 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76915818 - End of configuration. [testng] [2024-12-24 03:50:48,301] [pool-1-thread-9] Initializing /data/qa-7936/02 - not working.msr: [testng] 03:50:48,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:50:48,302 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:48,302 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-24_03-50-48.log] [testng] 03:50:48,302 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5801ac38 - End of configuration. [testng] [2024-12-24 03:50:48,862] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] 03:50:48,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:50:48,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:48,863 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-24_03-50-48.log] [testng] 03:50:48,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d5cf032 - End of configuration. [testng] [2024-12-24 03:50:49,468] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps/02 - 500x500x105_1046x1046x57_1_875um_steps_11-34-02_PMT - PMT [PMT1] _C0.ome.tif: [testng] 03:50:49,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:50:49,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:49,469 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-24_03-50-49.log] [testng] 03:50:49,469 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7bbcaf40 - End of configuration. [testng] [2024-12-24 03:50:52,126] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] 03:50:52,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:50:52,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:52,127 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-24_03-50-52.log] [testng] 03:50:52,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f4fefce - End of configuration. [testng] [2024-12-24 03:50:52,724] [pool-1-thread-5] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 03:50:52,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:50:52,725 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:52,725 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-24_03-50-52.log] [testng] 03:50:52,726 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51b60820 - End of configuration. [testng] [2024-12-24 03:50:53,388] [pool-1-thread-4] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 03:50:53,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:50:53,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:53,389 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-24_03-50-53.log] [testng] 03:50:53,389 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30099e7d - End of configuration. [testng] [2024-12-24 03:50:54,052] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 03:50:54,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:50:54,052 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:54,053 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-24_03-50-54.log] [testng] 03:50:54,075 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1e87e718 - End of configuration. [testng] [2024-12-24 03:50:54,740] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 03:50:54,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:50:54,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:50:54,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-24_03-50-54.log] [testng] 03:50:54,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@700b14f6 - End of configuration. [testng] [2024-12-24 03:51:02,521] [pool-1-thread-8] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-12-24 03:51:03,189] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-12-24 03:51:03,855] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-12-24 03:51:04,539] [pool-1-thread-2] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-12-24 03:51:05,221] [pool-1-thread-12] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-12-24 03:51:05,903] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-12-24 03:51:06,620] [pool-1-thread-9] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-12-24 03:51:07,354] [pool-1-thread-5] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-12-24 03:51:08,108] [pool-1-thread-4] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-12-24 03:51:08,807] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-12-24 03:51:10,675] [pool-1-thread-11] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] [2024-12-24 03:51:16,068] [pool-1-thread-10] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2024-12-24 03:51:16,894] [pool-1-thread-5] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2024-12-24 03:51:17,657] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-12-24 03:51:18,873] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-12-24 03:51:19,555] [pool-1-thread-3] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 1 minute 34 seconds Finished: SUCCESS