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Started by upstream project "BIOFORMATS-test-repo" build number 17 originally caused by: Started by upstream project "Trigger" build number 20 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins10189791951687608283.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_2062_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 01:13:05,012 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:13:05,014 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:13:05,014 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:13:05,015 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:13:05,015 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:13:05,016 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:13:05,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:13:05,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:13:05,016 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:13:05,017 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:13:05,017 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:13:05,017 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:13:05,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:13:05,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:13:05,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:13:05,212 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:13:05,217 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:13:05,218 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:13:05,218 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:13:05,219 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:13:05,219 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:13:05,219 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:13:05,219 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-30 01:13:05,228] [main] java.version = 11.0.16 [testng] 01:13:05,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:13:05,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:05,274 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-30_01-13-05.log] [testng] 01:13:05,276 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-03-30 01:13:05,278] [main] testng.directory = /data [testng] [2024-03-30 01:13:05,278] [main] testng.configDirectory = /config [testng] [2024-03-30 01:13:05,288] [main] testng.multiplier = 1.0 [testng] [2024-03-30 01:13:05,289] [main] testng.in-memory = false [testng] [2024-03-30 01:13:05,289] [main] testng.allow-missing = false [testng] [2024-03-30 01:13:05,289] [main] user.language = en [testng] [2024-03-30 01:13:05,289] [main] user.country = ${user.country} [testng] [2024-03-30 01:13:05,290] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-30 01:13:07,118] [main] ---------------------------------------- [testng] [2024-03-30 01:13:07,118] [main] Total files: 29 [testng] [2024-03-30 01:13:07,118] [main] Scan time: 1.828 s (63 ms/file) [testng] [2024-03-30 01:13:07,118] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-30 01:13:12,782] [pool-1-thread-1] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] 01:13:12,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:13:12,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:12,785 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-30_01-13-12.log] [testng] 01:13:12,786 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ad61e62 - End of configuration. [testng] [2024-03-30 01:13:12,855] [pool-1-thread-12] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] 01:13:12,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:13:12,856 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:12,857 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-30_01-13-12.log] [testng] 01:13:12,857 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e6bcf6 - End of configuration. [testng] [2024-03-30 01:13:12,903] [pool-1-thread-11] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 01:13:12,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:13:12,903 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:12,904 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-30_01-13-12.log] [testng] 01:13:12,904 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46ea62f9 - End of configuration. [testng] [2024-03-30 01:13:12,960] [pool-1-thread-10] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] 01:13:12,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:13:12,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:12,960 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-30_01-13-12.log] [testng] 01:13:12,961 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60fde3df - End of configuration. [testng] [2024-03-30 01:13:13,005] [pool-1-thread-9] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] 01:13:13,005 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:13:13,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,006 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-30_01-13-13.log] [testng] 01:13:13,007 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7980fa1e - End of configuration. [testng] [2024-03-30 01:13:13,033] [pool-1-thread-8] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] 01:13:13,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:13:13,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,033 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-30_01-13-13.log] [testng] 01:13:13,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4fb4da9f - End of configuration. [testng] [2024-03-30 01:13:13,067] [pool-1-thread-7] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] 01:13:13,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:13:13,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-30_01-13-13.log] [testng] 01:13:13,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4423a6 - End of configuration. [testng] [2024-03-30 01:13:13,160] [pool-1-thread-6] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.msr: [testng] 01:13:13,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:13:13,161 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,162 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-30_01-13-13.log] [testng] 01:13:13,162 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38cbb5b8 - End of configuration. [testng] [2024-03-30 01:13:13,196] [pool-1-thread-5] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 01:13:13,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:13:13,196 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,197 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-30_01-13-13.log] [testng] 01:13:13,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57ca311f - End of configuration. [testng] [2024-03-30 01:13:13,232] [pool-1-thread-4] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] 01:13:13,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:13:13,233 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-30_01-13-13.log] [testng] 01:13:13,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5649201c - End of configuration. [testng] [2024-03-30 01:13:13,296] [pool-1-thread-3] Initializing /data/qa-7936/02 - not working.msr: [testng] 01:13:13,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:13:13,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,297 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-30_01-13-13.log] [testng] 01:13:13,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a12faf - End of configuration. [testng] [2024-03-30 01:13:13,342] [pool-1-thread-2] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 01:13:13,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:13:13,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:13,343 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-30_01-13-13.log] [testng] 01:13:13,343 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78afb81c - End of configuration. [testng] [2024-03-30 01:13:15,825] [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] [2024-03-30 01:13:16,105] [pool-1-thread-12] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-03-30 01:13:16,136] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-03-30 01:13:16,161] [pool-1-thread-10] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-03-30 01:13:16,184] [pool-1-thread-4] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] [2024-03-30 01:13:16,216] [pool-1-thread-5] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] [2024-03-30 01:13:16,238] [pool-1-thread-8] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-03-30 01:13:16,260] [pool-1-thread-1] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-03-30 01:13:16,282] [pool-1-thread-6] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] [2024-03-30 01:13:16,308] [pool-1-thread-7] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-03-30 01:13:16,329] [pool-1-thread-11] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-03-30 01:13:16,623] [pool-1-thread-11] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] [2024-03-30 01:13:16,690] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] [2024-03-30 01:13:16,884] [pool-1-thread-4] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-03-30 01:13:17,097] [pool-1-thread-10] Initializing /data/qa-7936/01 - working.msr: [testng] [2024-03-30 01:13:17,130] [pool-1-thread-6] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1484, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 17 seconds Finished: SUCCESS