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Started by upstream project "BIOFORMATS-test-repo" build number 234 originally caused by: Started by upstream project "Trigger" build number 259 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins17277905579917138789.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_36814_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] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test test-automated: [testng] File leak detector installed [testng] 03:42:27,503 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:42:27,505 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 03:42:27,505 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:42:27,506 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:42:27,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:42:27,506 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:42:27,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 03:42:27,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:42:27,507 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:42:27,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:42:27,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:42:27,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:42:27,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:42:27,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:42:27,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:42:27,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:42:27,764 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:42:27,764 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:42:27,765 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:42:27,765 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:42:27,765 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 03:42:27,766 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 03:42:27,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 259 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-25 03:42:27,775] [main] java.version = 1.8.0_342 [testng] 03:42:27,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:42:27,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:27,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-25_03-42-27.log] [testng] 03:42:27,824 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-10-25 03:42:27,826] [main] testng.directory = /data [testng] [2024-10-25 03:42:27,827] [main] testng.configDirectory = /config [testng] [2024-10-25 03:42:27,838] [main] testng.multiplier = 1.0 [testng] [2024-10-25 03:42:27,839] [main] testng.in-memory = false [testng] [2024-10-25 03:42:27,839] [main] testng.allow-missing = false [testng] [2024-10-25 03:42:27,839] [main] user.language = en [testng] [2024-10-25 03:42:27,839] [main] user.country = ${user.country} [testng] [2024-10-25 03:42:27,839] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-25 03:42:32,289] [main] ---------------------------------------- [testng] [2024-10-25 03:42:32,289] [main] Total files: 29 [testng] [2024-10-25 03:42:32,290] [main] Scan time: 4.45 s (153 ms/file) [testng] [2024-10-25 03:42:32,290] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-25 03:42:40,901] [pool-1-thread-1] Initializing /data/qa-7936/02 - not working.msr: [testng] 03:42:40,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:42:40,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:40,903 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-25_03-42-40.log] [testng] 03:42:40,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33ec744 - End of configuration. [testng] [2024-10-25 03:42:41,030] [pool-1-thread-12] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 03:42:41,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:42:41,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,031 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-25_03-42-41.log] [testng] 03:42:41,032 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12b66476 - End of configuration. [testng] [2024-10-25 03:42:41,162] [pool-1-thread-11] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 03:42:41,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:42:41,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-25_03-42-41.log] [testng] 03:42:41,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52d66036 - End of configuration. [testng] [2024-10-25 03:42:41,287] [pool-1-thread-10] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 03:42:41,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:42:41,287 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,288 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-25_03-42-41.log] [testng] 03:42:41,288 |-INFO in ch.qos.logback.core.sift.SiftProcessor@20e83890 - End of configuration. [testng] [2024-10-25 03:42:41,414] [pool-1-thread-9] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 03:42:41,414 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:42:41,415 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,415 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-25_03-42-41.log] [testng] 03:42:41,416 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10f645c2 - End of configuration. [testng] [2024-10-25 03:42:41,506] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 03:42:41,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:42:41,506 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,507 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-25_03-42-41.log] [testng] 03:42:41,507 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23e60085 - End of configuration. [testng] [2024-10-25 03:42:41,625] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 03:42:41,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:42:41,626 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,626 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-25_03-42-41.log] [testng] 03:42:41,627 |-INFO in ch.qos.logback.core.sift.SiftProcessor@704422db - End of configuration. [testng] [2024-10-25 03:42:41,978] [pool-1-thread-6] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 03:42:41,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:42:41,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:41,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-25_03-42-41.log] [testng] 03:42:41,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@437110b7 - End of configuration. [testng] [2024-10-25 03:42:42,123] [pool-1-thread-5] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 03:42:42,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:42:42,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:42,124 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-25_03-42-42.log] [testng] 03:42:42,125 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32a5ae91 - End of configuration. [testng] [2024-10-25 03:42:42,265] [pool-1-thread-4] 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] 03:42:42,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:42:42,265 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:42,266 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-25_03-42-42.log] [testng] 03:42:42,266 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c63cad2 - End of configuration. [testng] [2024-10-25 03:42:42,942] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 03:42:42,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:42:42,942 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:42,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-25_03-42-42.log] [testng] 03:42:42,959 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2881f37 - End of configuration. [testng] [2024-10-25 03:42:43,094] [pool-1-thread-2] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 03:42:43,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:42:43,094 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:42:43,095 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-25_03-42-43.log] [testng] 03:42:43,095 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35b1eca8 - End of configuration. [testng] [2024-10-25 03:42:46,733] [pool-1-thread-3] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-10-25 03:42:46,869] [pool-1-thread-8] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-10-25 03:42:47,005] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-10-25 03:42:47,136] [pool-1-thread-12] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-10-25 03:42:47,247] [pool-1-thread-2] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-10-25 03:42:47,342] [pool-1-thread-9] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-10-25 03:42:47,448] [pool-1-thread-11] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-10-25 03:42:47,572] [pool-1-thread-10] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-10-25 03:42:47,682] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-10-25 03:42:47,782] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-10-25 03:42:48,496] [pool-1-thread-7] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] [2024-10-25 03:42:49,622] [pool-1-thread-2] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-10-25 03:42:50,412] [pool-1-thread-8] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-10-25 03:42:50,685] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-10-25 03:42:50,882] [pool-1-thread-10] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-10-25 03:42:51,046] [pool-1-thread-11] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 31 seconds Finished: SUCCESS