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Started by upstream project "BIOFORMATS-test-repo" build number 388 originally caused by: Started by upstream project "Trigger" build number 411 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@18 [BIOFORMATS-test-folder@18] $ /bin/bash -xe /tmp/jenkins741149134729506783.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61444_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 [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] 1 warning test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 02:40:45,756 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:40:45,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 02:40:45,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:40:45,758 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:40:45,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:40:45,759 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:40:45,760 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:40:45,760 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:40:45,760 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:40:45,761 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:40:45,761 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:40:45,761 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:40:45,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:40:45,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:40:45,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:40:45,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:40:45,957 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:40:45,957 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:40:45,957 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:40:45,958 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:40:45,958 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 02:40:45,959 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 02:40:45,959 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-23 02:40:45,968] [main] java.version = 17.0.2 [testng] 02:40:45,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:40:45,971 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:40:46,016 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-23_02-40-45.log] [testng] 02:40:46,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-23 02:40:46,019] [main] testng.directory = /data [testng] [2025-03-23 02:40:46,020] [main] testng.configDirectory = /config [testng] [2025-03-23 02:40:46,029] [main] testng.multiplier = 1.0 [testng] [2025-03-23 02:40:46,030] [main] testng.in-memory = false [testng] [2025-03-23 02:40:46,030] [main] testng.allow-missing = false [testng] [2025-03-23 02:40:46,030] [main] user.language = en [testng] [2025-03-23 02:40:46,030] [main] user.country = ${user.country} [testng] [2025-03-23 02:40:46,030] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-23 02:41:53,842] [main] ---------------------------------------- [testng] [2025-03-23 02:41:53,842] [main] Total files: 31 [testng] [2025-03-23 02:41:53,842] [main] Scan time: 67.812 s (2187 ms/file) [testng] [2025-03-23 02:41:53,843] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 29 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-23 02:43:24,632] [pool-1-thread-1] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] 02:43:24,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:43:24,632 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:24,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-23_02-43-24.log] [testng] 02:43:24,634 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71340f6b - End of configuration. [testng] [2025-03-23 02:43:27,472] [pool-1-thread-12] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 02:43:27,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:43:27,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:27,473 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-23_02-43-27.log] [testng] 02:43:27,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d98041d - End of configuration. [testng] [2025-03-23 02:43:30,251] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 02:43:30,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:43:30,252 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:30,252 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-23_02-43-30.log] [testng] 02:43:30,253 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c104e4a - End of configuration. [testng] [2025-03-23 02:43:33,385] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 02:43:33,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:43:33,385 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:33,385 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-23_02-43-33.log] [testng] 02:43:33,386 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17622459 - End of configuration. [testng] [2025-03-23 02:43:36,292] [pool-1-thread-9] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 02:43:36,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:43:36,293 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:36,293 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-23_02-43-36.log] [testng] 02:43:36,294 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64d8d3 - End of configuration. [testng] [2025-03-23 02:43:39,104] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] 02:43:39,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:43:39,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:39,106 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-23_02-43-39.log] [testng] 02:43:39,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@597d7b9e - End of configuration. [testng] [2025-03-23 02:43:41,433] [pool-1-thread-7] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 02:43:41,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:43:41,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:41,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-23_02-43-41.log] [testng] 02:43:41,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@82423be - End of configuration. [testng] [2025-03-23 02:43:42,737] [pool-1-thread-6] Initializing /data/qa-7936/01 - working.msr: [testng] 02:43:42,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:43:42,738 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:42,738 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-23_02-43-42.log] [testng] 02:43:42,739 |-INFO in ch.qos.logback.core.sift.SiftProcessor@93bb044 - End of configuration. [testng] [2025-03-23 02:43:44,559] [pool-1-thread-5] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 02:43:44,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:43:44,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:44,560 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-23_02-43-44.log] [testng] 02:43:44,561 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6461c61b - End of configuration. [testng] [2025-03-23 02:43:47,037] [pool-1-thread-4] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] 02:43:47,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:43:47,037 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:47,038 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-23_02-43-47.log] [testng] 02:43:47,038 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ceb52da - End of configuration. [testng] [2025-03-23 02:43:49,515] [pool-1-thread-3] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] 02:43:49,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:43:49,515 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:49,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-23_02-43-49.log] [testng] 02:43:49,517 |-INFO in ch.qos.logback.core.sift.SiftProcessor@265717db - End of configuration. [testng] [2025-03-23 02:43:52,416] [pool-1-thread-2] Initializing /data/public/zenodo-10476252/test.msr: [testng] 02:43:52,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:43:52,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:43:52,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-23_02-43-52.log] [testng] 02:43:52,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57de55f6 - End of configuration. [testng] [2025-03-23 02:44:12,673] [pool-1-thread-1] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2025-03-23 02:44:15,001] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2025-03-23 02:44:17,516] [pool-1-thread-8] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2025-03-23 02:44:19,635] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2025-03-23 02:44:23,253] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2025-03-23 02:44:25,411] [pool-1-thread-7] Initializing /data/qa-7936/02 - not working.msr: [testng] [2025-03-23 02:44:27,645] [pool-1-thread-4] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2025-03-23 02:44:30,020] [pool-1-thread-9] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2025-03-23 02:44:32,180] [pool-1-thread-2] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] [2025-03-23 02:44:34,320] [pool-1-thread-5] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2025-03-23 02:44:36,655] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2025-03-23 02:44:39,133] [pool-1-thread-10] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2025-03-23 02:44:58,805] [pool-1-thread-9] 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] [2025-03-23 02:45:09,866] [pool-1-thread-11] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2025-03-23 02:45:11,800] [pool-1-thread-5] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2025-03-23 02:45:13,124] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2025-03-23 02:45:14,501] [pool-1-thread-3] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1537, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 5 minutes 55 seconds Finished: SUCCESS