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Started by upstream project "BIOFORMATS-test-repo" build number 261 originally caused by: Started by upstream project "Trigger" build number 285 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins11630006175230820200.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41242_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] 03:58:18,888 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 03:58:18,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 03:58:18,890 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:58:18,891 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 03:58:18,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 03:58:18,891 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 03:58:18,892 |-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] 03:58:18,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:58:18,892 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 03:58:18,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 03:58:18,893 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 03:58:18,894 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 03:58:19,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 03:58:19,062 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 03:58:19,084 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 03:58:19,085 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 03:58:19,090 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 03:58:19,090 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 03:58:19,090 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 03:58:19,091 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 03:58:19,091 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 03:58:19,092 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 03:58:19,092 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 200 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-20 03:58:19,101] [main] java.version = 17.0.2 [testng] 03:58:19,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:58:19,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:58:19,146 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-20_03-58-19.log] [testng] 03:58:19,148 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-20 03:58:19,150] [main] testng.directory = /data [testng] [2024-11-20 03:58:19,150] [main] testng.configDirectory = /config [testng] [2024-11-20 03:58:19,159] [main] testng.multiplier = 1.0 [testng] [2024-11-20 03:58:19,159] [main] testng.in-memory = false [testng] [2024-11-20 03:58:19,159] [main] testng.allow-missing = false [testng] [2024-11-20 03:58:19,160] [main] user.language = en [testng] [2024-11-20 03:58:19,160] [main] user.country = ${user.country} [testng] [2024-11-20 03:58:19,160] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-20 03:58:35,604] [main] ---------------------------------------- [testng] [2024-11-20 03:58:35,604] [main] Total files: 29 [testng] [2024-11-20 03:58:35,604] [main] Scan time: 16.443 s (567 ms/file) [testng] [2024-11-20 03:58:35,604] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-20 03:59:04,646] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] 03:59:04,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 03:59:04,646 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:04,647 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-20_03-59-04.log] [testng] 03:59:04,648 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2657000c - End of configuration. [testng] [2024-11-20 03:59:05,298] [pool-1-thread-12] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] 03:59:05,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 03:59:05,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:05,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-20_03-59-05.log] [testng] 03:59:05,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c205b2e - End of configuration. [testng] [2024-11-20 03:59:06,266] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] 03:59:06,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 03:59:06,266 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:06,267 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-20_03-59-06.log] [testng] 03:59:06,268 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c104e4a - End of configuration. [testng] [2024-11-20 03:59:06,937] [pool-1-thread-10] Initializing /data/qa-7936/01 - working.msr: [testng] 03:59:06,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 03:59:06,937 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:06,938 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-20_03-59-06.log] [testng] 03:59:06,939 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6835131a - End of configuration. [testng] [2024-11-20 03:59:07,677] [pool-1-thread-9] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] 03:59:07,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 03:59:07,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:07,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-20_03-59-07.log] [testng] 03:59:07,679 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71c0d3fa - End of configuration. [testng] [2024-11-20 03:59:08,565] [pool-1-thread-8] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] 03:59:08,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 03:59:08,566 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:08,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-20_03-59-08.log] [testng] 03:59:08,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dc44c32 - End of configuration. [testng] [2024-11-20 03:59:09,144] [pool-1-thread-7] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] 03:59:09,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 03:59:09,144 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:09,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-20_03-59-09.log] [testng] 03:59:09,145 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55c2ed88 - End of configuration. [testng] [2024-11-20 03:59:09,979] [pool-1-thread-6] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 03:59:09,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 03:59:09,979 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:09,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-20_03-59-09.log] [testng] 03:59:09,980 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ba18eba - End of configuration. [testng] [2024-11-20 03:59:10,820] [pool-1-thread-5] Initializing /data/qa-7936/02 - not working.msr: [testng] 03:59:10,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 03:59:10,820 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:10,821 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-20_03-59-10.log] [testng] 03:59:10,821 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57217f06 - End of configuration. [testng] [2024-11-20 03:59:11,521] [pool-1-thread-4] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 03:59:11,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 03:59:11,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:11,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-20_03-59-11.log] [testng] 03:59:11,522 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3fbb8180 - End of configuration. [testng] [2024-11-20 03:59:12,067] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 03:59:12,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 03:59:12,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:12,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-20_03-59-12.log] [testng] 03:59:12,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@98b88cd - End of configuration. [testng] [2024-11-20 03:59:12,709] [pool-1-thread-2] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] 03:59:12,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 03:59:12,709 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:59:12,710 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-20_03-59-12.log] [testng] 03:59:12,711 |-INFO in ch.qos.logback.core.sift.SiftProcessor@135cea30 - End of configuration. [testng] [2024-11-20 03:59:20,648] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-11-20 03:59:21,572] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-11-20 03:59:22,238] [pool-1-thread-1] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-11-20 03:59:23,078] [pool-1-thread-7] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] [2024-11-20 03:59:24,791] [pool-1-thread-10] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-11-20 03:59:25,559] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-11-20 03:59:26,187] [pool-1-thread-6] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-11-20 03:59:26,830] [pool-1-thread-5] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2024-11-20 03:59:27,801] [pool-1-thread-12] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-11-20 03:59:28,798] [pool-1-thread-3] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2024-11-20 03:59:29,774] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-11-20 03:59:30,761] [pool-1-thread-2] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-11-20 03:59:36,505] [pool-1-thread-8] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-11-20 03:59:37,534] [pool-1-thread-6] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] [2024-11-20 03:59:38,201] [pool-1-thread-12] 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] [2024-11-20 03:59:41,525] [pool-1-thread-5] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.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 50 seconds Finished: SUCCESS