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Started by upstream project "BIOFORMATS-test-repo" build number 184 originally caused by: Started by upstream project "Trigger" build number 206 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins17317017945532249480.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_29130_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] 11:36:48,864 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 11:36:48,865 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 11:36:48,865 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:36:48,866 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 11:36:48,867 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 11:36:48,867 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 11:36:48,867 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 11:36:48,867 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:36:48,868 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 11:36:48,868 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 11:36:48,868 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 11:36:48,869 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 11:36:49,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 11:36:49,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 11:36:49,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 11:36:49,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 11:36:49,054 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 11:36:49,055 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 11:36:49,055 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 11:36:49,055 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 11:36:49,055 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 11:36:49,056 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 11:36:49,056 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 188 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-09-11 11:36:49,065] [main] java.version = 17.0.2 [testng] 11:36:49,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 11:36:49,068 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:49,108 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-09-11_11-36-49.log] [testng] 11:36:49,109 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-09-11 11:36:49,111] [main] testng.directory = /data [testng] [2024-09-11 11:36:49,111] [main] testng.configDirectory = /config [testng] [2024-09-11 11:36:49,120] [main] testng.multiplier = 1.0 [testng] [2024-09-11 11:36:49,121] [main] testng.in-memory = false [testng] [2024-09-11 11:36:49,121] [main] testng.allow-missing = false [testng] [2024-09-11 11:36:49,121] [main] user.language = en [testng] [2024-09-11 11:36:49,121] [main] user.country = ${user.country} [testng] [2024-09-11 11:36:49,121] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-09-11 11:36:51,526] [main] ---------------------------------------- [testng] [2024-09-11 11:36:51,526] [main] Total files: 29 [testng] [2024-09-11 11:36:51,526] [main] Scan time: 2.405 s (82 ms/file) [testng] [2024-09-11 11:36:51,526] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-09-11 11:36:57,360] [pool-1-thread-1] Initializing /data/qa-7936/01 - working.msr: [testng] 11:36:57,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 11:36:57,361 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,362 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-09-11_11-36-57.log] [testng] 11:36:57,363 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d010d62 - End of configuration. [testng] [2024-09-11 11:36:57,432] [pool-1-thread-12] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] 11:36:57,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 11:36:57,432 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-09-11_11-36-57.log] [testng] 11:36:57,434 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f784807 - End of configuration. [testng] [2024-09-11 11:36:57,496] [pool-1-thread-11] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] 11:36:57,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:36:57,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-09-11_11-36-57.log] [testng] 11:36:57,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@a00fff - End of configuration. [testng] [2024-09-11 11:36:57,534] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] 11:36:57,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 11:36:57,534 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,535 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-09-11_11-36-57.log] [testng] 11:36:57,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5701d3da - End of configuration. [testng] [2024-09-11 11:36:57,577] [pool-1-thread-9] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 11:36:57,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 11:36:57,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-09-11_11-36-57.log] [testng] 11:36:57,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@739d6f3b - End of configuration. [testng] [2024-09-11 11:36:57,639] [pool-1-thread-8] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 11:36:57,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 11:36:57,639 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-09-11_11-36-57.log] [testng] 11:36:57,640 |-INFO in ch.qos.logback.core.sift.SiftProcessor@232c1846 - End of configuration. [testng] [2024-09-11 11:36:57,681] [pool-1-thread-7] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 11:36:57,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:36:57,681 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,682 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-09-11_11-36-57.log] [testng] 11:36:57,683 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63334554 - End of configuration. [testng] [2024-09-11 11:36:57,751] [pool-1-thread-6] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 11:36:57,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 11:36:57,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,753 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-09-11_11-36-57.log] [testng] 11:36:57,753 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78cacc96 - End of configuration. [testng] [2024-09-11 11:36:57,786] [pool-1-thread-5] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 11:36:57,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 11:36:57,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-09-11_11-36-57.log] [testng] 11:36:57,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@170c40cc - End of configuration. [testng] [2024-09-11 11:36:57,875] [pool-1-thread-4] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] 11:36:57,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 11:36:57,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-09-11_11-36-57.log] [testng] 11:36:57,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@152cc1a4 - End of configuration. [testng] [2024-09-11 11:36:57,902] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 11:36:57,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 11:36:57,902 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:57,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-09-11_11-36-57.log] [testng] 11:36:57,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5eebd31d - End of configuration. [testng] [2024-09-11 11:36:58,228] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] 11:36:58,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 11:36:58,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:36:58,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-09-11_11-36-58.log] [testng] 11:36:58,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27f97de7 - End of configuration. [testng] [2024-09-11 11:37:00,382] [pool-1-thread-4] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-09-11 11:37:00,522] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-09-11 11:37:00,553] [pool-1-thread-5] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-09-11 11:37:00,595] [pool-1-thread-8] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-09-11 11:37:00,661] [pool-1-thread-7] Initializing /data/qa-7936/02 - not working.msr: [testng] [2024-09-11 11:37:00,708] [pool-1-thread-12] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-09-11 11:37:00,988] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-09-11 11:37:01,024] [pool-1-thread-9] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] [2024-09-11 11:37:01,102] [pool-1-thread-2] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-09-11 11:37:01,135] [pool-1-thread-1] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] [2024-09-11 11:37:01,585] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] [2024-09-11 11:37:01,743] [pool-1-thread-2] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-09-11 11:37:01,823] [pool-1-thread-7] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-09-11 11:37:01,864] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [2024-09-11 11:37:01,891] [pool-1-thread-11] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-09-11 11:37:01,942] [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] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 21 seconds Finished: SUCCESS