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Started by upstream project "BIOFORMATS-test-repo" build number 219 originally caused by: Started by upstream project "Trigger" build number 246 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins7162896424121236617.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_34818_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] 05:08:29,322 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 05:08:29,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 05:08:29,323 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:08:29,324 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 05:08:29,325 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 05:08:29,325 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 05:08:29,325 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 05:08:29,325 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:08:29,326 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 05:08:29,326 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 05:08:29,326 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 05:08:29,327 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 05:08:29,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 05:08:29,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 05:08:29,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 05:08:29,512 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 05:08:29,517 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 05:08:29,517 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 05:08:29,517 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 05:08:29,517 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 05:08:29,518 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 05:08:29,519 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 05:08:29,519 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-13 05:08:29,527] [main] java.version = 17.0.2 [testng] 05:08:29,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 05:08:29,531 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:08:29,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-13_05-08-29.log] [testng] 05:08:29,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-13 05:08:29,575] [main] testng.directory = /data [testng] [2024-10-13 05:08:29,575] [main] testng.configDirectory = /config [testng] [2024-10-13 05:08:29,583] [main] testng.multiplier = 1.0 [testng] [2024-10-13 05:08:29,584] [main] testng.in-memory = false [testng] [2024-10-13 05:08:29,584] [main] testng.allow-missing = false [testng] [2024-10-13 05:08:29,584] [main] user.language = en [testng] [2024-10-13 05:08:29,584] [main] user.country = ${user.country} [testng] [2024-10-13 05:08:29,584] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-13 05:08:45,492] [main] ---------------------------------------- [testng] [2024-10-13 05:08:45,492] [main] Total files: 29 [testng] [2024-10-13 05:08:45,492] [main] Scan time: 15.907 s (548 ms/file) [testng] [2024-10-13 05:08:45,492] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-13 05:09:09,506] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] 05:09:09,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 05:09:09,507 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:09,508 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-13_05-09-09.log] [testng] 05:09:09,508 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54723e28 - End of configuration. [testng] [2024-10-13 05:09:10,099] [pool-1-thread-12] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] 05:09:10,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 05:09:10,099 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:10,100 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-13_05-09-10.log] [testng] 05:09:10,100 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6461c61b - End of configuration. [testng] [2024-10-13 05:09:10,723] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] 05:09:10,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 05:09:10,723 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:10,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-13_05-09-10.log] [testng] 05:09:10,724 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57de55f6 - End of configuration. [testng] [2024-10-13 05:09:11,297] [pool-1-thread-10] Initializing /data/qa-7936/01 - working.msr: [testng] 05:09:11,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 05:09:11,297 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:11,298 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-13_05-09-11.log] [testng] 05:09:11,298 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dc44c32 - End of configuration. [testng] [2024-10-13 05:09:11,865] [pool-1-thread-9] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 05:09:11,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 05:09:11,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:11,865 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-13_05-09-11.log] [testng] 05:09:11,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@493a83c9 - End of configuration. [testng] [2024-10-13 05:09:12,510] [pool-1-thread-8] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] 05:09:12,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 05:09:12,510 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:12,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-13_05-09-12.log] [testng] 05:09:12,511 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16dc038c - End of configuration. [testng] [2024-10-13 05:09:13,109] [pool-1-thread-7] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] 05:09:13,109 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 05:09:13,110 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:13,110 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-13_05-09-13.log] [testng] 05:09:13,111 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f7f57ff - End of configuration. [testng] [2024-10-13 05:09:13,669] [pool-1-thread-6] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 05:09:13,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 05:09:13,669 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:13,670 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-13_05-09-13.log] [testng] 05:09:13,670 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d3f1905 - End of configuration. [testng] [2024-10-13 05:09:14,294] [pool-1-thread-5] Initializing /data/qa-7936/02 - not working.msr: [testng] 05:09:14,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 05:09:14,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:14,295 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-13_05-09-14.log] [testng] 05:09:14,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@500dabb6 - End of configuration. [testng] [2024-10-13 05:09:14,839] [pool-1-thread-4] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 05:09:14,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 05:09:14,839 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:14,840 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-13_05-09-14.log] [testng] 05:09:14,840 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f784807 - End of configuration. [testng] [2024-10-13 05:09:15,333] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 05:09:15,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 05:09:15,333 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:15,334 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-13_05-09-15.log] [testng] 05:09:15,334 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a00fff - End of configuration. [testng] [2024-10-13 05:09:15,874] [pool-1-thread-2] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] 05:09:15,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 05:09:15,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 05:09:15,875 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-13_05-09-15.log] [testng] 05:09:15,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5701d3da - End of configuration. [testng] [2024-10-13 05:09:22,735] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-10-13 05:09:23,331] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-10-13 05:09:23,952] [pool-1-thread-1] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-10-13 05:09:24,585] [pool-1-thread-7] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-10-13 05:09:25,201] [pool-1-thread-4] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2024-10-13 05:09:26,219] [pool-1-thread-10] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-10-13 05:09:26,838] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-10-13 05:09:27,441] [pool-1-thread-5] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-10-13 05:09:28,042] [pool-1-thread-6] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2024-10-13 05:09:28,629] [pool-1-thread-9] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-10-13 05:09:29,138] [pool-1-thread-3] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2024-10-13 05:09:30,706] [pool-1-thread-2] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-10-13 05:09:34,870] [pool-1-thread-8] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-10-13 05:09:35,544] [pool-1-thread-6] 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] [2024-10-13 05:09:38,258] [pool-1-thread-3] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-10-13 05:09:38,893] [pool-1-thread-10] Initializing /data/qa-7992/NegativeArraySizeException_small.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 36 seconds Finished: SUCCESS