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Started by upstream project "BIOFORMATS-test-repo" build number 255 originally caused by: Started by upstream project "Trigger" build number 279 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins14234457476486290776.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40258_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 02:59:16,768 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:59:16,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 02:59:16,769 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:59:16,770 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:59:16,770 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:59:16,771 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:59:16,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:59:16,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:59:16,771 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:59:16,772 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:59:16,772 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:59:16,772 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:59:16,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:59:16,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:59:16,956 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:59:16,957 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:59:16,963 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:59:16,963 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:59:16,963 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:59:16,964 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:59:16,964 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 02:59:16,964 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 02:59:16,965 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-14 02:59:16,974] [main] java.version = 21 [testng] 02:59:16,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:59:16,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:17,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-14_02-59-16.log] [testng] 02:59:17,020 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-14 02:59:17,022] [main] testng.directory = /data [testng] [2024-11-14 02:59:17,022] [main] testng.configDirectory = /config [testng] [2024-11-14 02:59:17,031] [main] testng.multiplier = 1.0 [testng] [2024-11-14 02:59:17,032] [main] testng.in-memory = false [testng] [2024-11-14 02:59:17,032] [main] testng.allow-missing = false [testng] [2024-11-14 02:59:17,032] [main] user.language = en [testng] [2024-11-14 02:59:17,032] [main] user.country = ${user.country} [testng] [2024-11-14 02:59:17,032] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-14 02:59:29,437] [main] ---------------------------------------- [testng] [2024-11-14 02:59:29,437] [main] Total files: 29 [testng] [2024-11-14 02:59:29,437] [main] Scan time: 12.405 s (427 ms/file) [testng] [2024-11-14 02:59:29,438] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-14 02:59:50,423] [pool-1-thread-1] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 02:59:50,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:59:50,423 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:50,424 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-14_02-59-50.log] [testng] 02:59:50,424 |-INFO in ch.qos.logback.core.sift.SiftProcessor@cc2268c - End of configuration. [testng] [2024-11-14 02:59:50,885] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] 02:59:50,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:59:50,886 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:50,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-14_02-59-50.log] [testng] 02:59:50,887 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dcecab8 - End of configuration. [testng] [2024-11-14 02:59:51,547] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 02:59:51,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:59:51,547 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:51,548 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-14_02-59-51.log] [testng] 02:59:51,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@791073f4 - End of configuration. [testng] [2024-11-14 02:59:52,092] [pool-1-thread-10] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 02:59:52,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:59:52,092 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:52,093 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-14_02-59-52.log] [testng] 02:59:52,093 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f731d9e - End of configuration. [testng] [2024-11-14 02:59:52,660] [pool-1-thread-9] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 02:59:52,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:59:52,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:52,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-14_02-59-52.log] [testng] 02:59:52,662 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45713032 - End of configuration. [testng] [2024-11-14 02:59:53,335] [pool-1-thread-8] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 02:59:53,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:59:53,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:53,335 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-14_02-59-53.log] [testng] 02:59:53,336 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17c0f395 - End of configuration. [testng] [2024-11-14 02:59:53,816] [pool-1-thread-7] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 02:59:53,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:59:53,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:53,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-14_02-59-53.log] [testng] 02:59:53,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d7d2440 - End of configuration. [testng] [2024-11-14 02:59:54,295] [pool-1-thread-6] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 02:59:54,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:59:54,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:54,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-14_02-59-54.log] [testng] 02:59:54,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6146f4ea - End of configuration. [testng] [2024-11-14 02:59:54,740] [pool-1-thread-5] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] 02:59:54,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:59:54,741 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:54,741 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-14_02-59-54.log] [testng] 02:59:54,742 |-INFO in ch.qos.logback.core.sift.SiftProcessor@640c18e5 - End of configuration. [testng] [2024-11-14 02:59:55,230] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 02:59:55,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:59:55,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:55,231 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-14_02-59-55.log] [testng] 02:59:55,232 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d19e416 - End of configuration. [testng] [2024-11-14 02:59:55,743] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 02:59:55,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:59:55,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:55,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-14_02-59-55.log] [testng] 02:59:55,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47ec6f89 - End of configuration. [testng] [2024-11-14 02:59:56,293] [pool-1-thread-2] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 02:59:56,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:59:56,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:59:56,294 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-14_02-59-56.log] [testng] 02:59:56,295 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4c2c081b - End of configuration. [testng] [2024-11-14 03:00:02,164] [pool-1-thread-4] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-11-14 03:00:02,693] [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] [2024-11-14 03:00:05,196] [pool-1-thread-1] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-11-14 03:00:05,619] [pool-1-thread-5] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-11-14 03:00:06,206] [pool-1-thread-10] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-11-14 03:00:06,879] [pool-1-thread-3] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2024-11-14 03:00:07,448] [pool-1-thread-8] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-11-14 03:00:07,873] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-11-14 03:00:08,260] [pool-1-thread-9] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-11-14 03:00:08,733] [pool-1-thread-2] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] [2024-11-14 03:00:09,143] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-11-14 03:00:09,730] [pool-1-thread-11] Initializing /data/qa-7936/02 - not working.msr: [testng] [2024-11-14 03:00:14,162] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-11-14 03:00:14,659] [pool-1-thread-5] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-11-14 03:00:15,836] [pool-1-thread-8] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-11-14 03:00:16,619] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [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 16 seconds Finished: SUCCESS