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Started by upstream project "BIOFORMATS-test-repo" build number 296 originally caused by: Started by upstream project "Trigger" build number 315 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins7656022246316115917.sh + '[' imspector = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46860_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 test-automated: [testng] File leak detector installed [testng] 04:14:05,211 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 04:14:05,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 04:14:05,213 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:14:05,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:14:05,214 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:14:05,214 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:14:05,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:14:05,214 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:14:05,215 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:14:05,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:14:05,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:14:05,215 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:14:05,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:14:05,429 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:14:05,456 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:14:05,457 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:14:05,464 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:14:05,464 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:14:05,465 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:14:05,465 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:14:05,465 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 04:14:05,466 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 04:14:05,466 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 251 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-20 04:14:05,475] [main] java.version = 1.8.0_342 [testng] 04:14:05,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:14:05,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:05,522 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-20_04-14-05.log] [testng] 04:14:05,523 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-20 04:14:05,525] [main] testng.directory = /data [testng] [2024-12-20 04:14:05,525] [main] testng.configDirectory = /config [testng] [2024-12-20 04:14:05,537] [main] testng.multiplier = 1.0 [testng] [2024-12-20 04:14:05,537] [main] testng.in-memory = false [testng] [2024-12-20 04:14:05,538] [main] testng.allow-missing = false [testng] [2024-12-20 04:14:05,538] [main] user.language = en [testng] [2024-12-20 04:14:05,538] [main] user.country = ${user.country} [testng] [2024-12-20 04:14:05,538] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-20 04:14:23,405] [main] ---------------------------------------- [testng] [2024-12-20 04:14:23,405] [main] Total files: 29 [testng] [2024-12-20 04:14:23,405] [main] Scan time: 17.866 s (616 ms/file) [testng] [2024-12-20 04:14:23,405] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 28 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-20 04:14:51,295] [pool-1-thread-1] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_FLIM_z-stack_1.msr: [testng] 04:14:51,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:14:51,295 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:51,296 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-20_04-14-51.log] [testng] 04:14:51,297 |-INFO in ch.qos.logback.core.sift.SiftProcessor@228c9a99 - End of configuration. [testng] [2024-12-20 04:14:52,188] [pool-1-thread-12] Initializing /data/qa-7936/01 - working.msr: [testng] 04:14:52,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:14:52,188 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:52,189 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-20_04-14-52.log] [testng] 04:14:52,189 |-INFO in ch.qos.logback.core.sift.SiftProcessor@341e4376 - End of configuration. [testng] [2024-12-20 04:14:52,815] [pool-1-thread-11] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - Arf_z-stack_FLIM_TDC_C0.ome.tif: [testng] 04:14:52,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:14:52,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:52,816 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-20_04-14-52.log] [testng] 04:14:52,817 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8a45ac - End of configuration. [testng] [2024-12-20 04:14:54,067] [pool-1-thread-10] Initializing /data/qa-7992/NegativeArraySizeException_small.msr: [testng] 04:14:54,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:14:54,067 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:54,068 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-20_04-14-54.log] [testng] 04:14:54,068 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68bb9f81 - End of configuration. [testng] [2024-12-20 04:14:54,754] [pool-1-thread-9] Initializing /data/qa-7936/02 - not working.msr: [testng] 04:14:54,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:14:54,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:54,755 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-20_04-14-54.log] [testng] 04:14:54,755 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb99b0b - End of configuration. [testng] [2024-12-20 04:14:55,387] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Lifetime file.msr: [testng] 04:14:55,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:14:55,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:55,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-20_04-14-55.log] [testng] 04:14:55,389 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e799487 - End of configuration. [testng] [2024-12-20 04:14:55,963] [pool-1-thread-7] 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] 04:14:55,963 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:14:55,964 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:55,964 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-20_04-14-55.log] [testng] 04:14:55,964 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10b83541 - End of configuration. [testng] [2024-12-20 04:14:59,130] [pool-1-thread-6] Initializing /data/qa-17102/1 channel binning 4 time series.msr: [testng] 04:14:59,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:14:59,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:59,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-20_04-14-59.log] [testng] 04:14:59,131 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e39d3b1 - End of configuration. [testng] [2024-12-20 04:14:59,898] [pool-1-thread-5] Initializing /data/qa-7992/ArrayIndexOutOfBoundsException.msr: [testng] 04:14:59,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:14:59,898 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:14:59,899 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-20_04-14-59.log] [testng] 04:14:59,899 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76b599e8 - End of configuration. [testng] [2024-12-20 04:15:00,516] [pool-1-thread-4] Initializing /data/qa-7658/Document1_13-09-25.msr: [testng] 04:15:00,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:15:00,517 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:15:00,517 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-20_04-15-00.log] [testng] 04:15:00,518 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7fd544f8 - End of configuration. [testng] [2024-12-20 04:15:01,173] [pool-1-thread-3] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel Zstack.msr: [testng] 04:15:01,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:15:01,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:15:01,173 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-20_04-15-01.log] [testng] 04:15:01,198 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1cd74a3e - End of configuration. [testng] [2024-12-20 04:15:01,877] [pool-1-thread-2] Initializing /data/qa-17102/2 channels FLIM z stack.msr: [testng] 04:15:01,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:15:01,877 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:15:01,877 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-20_04-15-01.log] [testng] 04:15:01,878 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76915818 - End of configuration. [testng] [2024-12-20 04:15:09,935] [pool-1-thread-1] Initializing /data/qa-11369/02 - 70 - 1 - tp1 - x16 TCSPC.msr: [testng] [2024-12-20 04:15:10,517] [pool-1-thread-8] Initializing /data/qa-17102/1 channel binning 8 time series.msr: [testng] [2024-12-20 04:15:11,391] [pool-1-thread-6] Initializing /data/paul/msr files - Paul Thomas UEA/Single channel single slice 4 tiles.msr: [testng] [2024-12-20 04:15:12,060] [pool-1-thread-2] Initializing /data/qa-11369/01 - 770nm FITC - HybridPMT.msr: [testng] [2024-12-20 04:15:12,763] [pool-1-thread-12] Initializing /data/qa-7992/IllegalArgumentException.msr: [testng] [2024-12-20 04:15:13,681] [pool-1-thread-10] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel single slice.msr: [testng] [2024-12-20 04:15:14,279] [pool-1-thread-9] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning.msr: [testng] [2024-12-20 04:15:14,910] [pool-1-thread-5] Initializing /data/qa-27309/181109_e3_cut.msr: [testng] [2024-12-20 04:15:15,521] [pool-1-thread-4] Initializing /data/qa-9468/HPDR10467U-40-VD0191-red-100pc-without-tube.msr: [testng] [2024-12-20 04:15:16,224] [pool-1-thread-3] Initializing /data/qa-7702/trim- scope msr z-stacks/02 - 500x500x105_1046x1046x57_1.875um_steps.msr: [testng] [2024-12-20 04:15:17,395] [pool-1-thread-11] Initializing /data/qa-17102/2 channels FLIM time series.msr: [testng] [2024-12-20 04:15:22,464] [pool-1-thread-5] Initializing /data/qa-7936/z-TC - for LOCI.msr: [testng] [2024-12-20 04:15:23,173] [pool-1-thread-10] Initializing /data/qa-4929/OMERO data/01 - urea_irf_image_TCSPC-data.msr: [testng] [2024-12-20 04:15:23,902] [pool-1-thread-1] Initializing /data/qa-7668/01 - RhodamineB - FLIM test - 4 binning_12-08-53_TCSPC_C0.ome.tif: [testng] [2024-12-20 04:15:25,153] [pool-1-thread-8] Initializing /data/paul/msr files - Paul Thomas UEA/Two channel Zstack.msr: [testng] [2024-12-20 04:15:25,916] [pool-1-thread-12] Initializing /data/qa-4929/OMERO data/01 - 27hpf_f2-GFP-wt1b+rfp-flk1 - 3channel-z-stack.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 32 seconds Finished: SUCCESS