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Started by upstream project "BIOFORMATS-test-repo" build number 268 originally caused by: Started by upstream project "Trigger" build number 291 originally caused by: Started by timer 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/jenkins9241296655651584787.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_42309_merge_ci -v /uod/idr/repos/curated/li-flim:/data -v /uod/idr-scratch/merge-ci/curated/li-flim:/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] 01:54:34,762 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:54:34,763 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:54:34,763 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:54:34,764 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:54:34,765 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:54:34,765 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:54:34,765 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:54:34,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:54:34,766 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:54:34,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:54:34,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:54:34,767 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:54:34,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:54:34,993 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:54:35,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:54:35,015 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:54:35,021 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:54:35,021 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:54:35,021 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:54:35,021 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:54:35,021 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:54:35,022 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:54:35,022 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 256 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-26 01:54:35,031] [main] java.version = 11.0.16 [testng] 01:54:35,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:54:35,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:54:35,075 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-26_01-54-35.log] [testng] 01:54:35,077 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-26 01:54:35,079] [main] testng.directory = /data [testng] [2024-11-26 01:54:35,079] [main] testng.configDirectory = /config [testng] [2024-11-26 01:54:35,089] [main] testng.multiplier = 1.0 [testng] [2024-11-26 01:54:35,090] [main] testng.in-memory = false [testng] [2024-11-26 01:54:35,090] [main] testng.allow-missing = false [testng] [2024-11-26 01:54:35,090] [main] user.language = en [testng] [2024-11-26 01:54:35,090] [main] user.country = ${user.country} [testng] [2024-11-26 01:54:35,090] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-26 01:54:58,957] [main] ---------------------------------------- [testng] [2024-11-26 01:54:58,957] [main] Total files: 28 [testng] [2024-11-26 01:54:58,957] [main] Scan time: 23.867 s (852 ms/file) [testng] [2024-11-26 01:54:58,957] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-26 01:56:50,653] [pool-1-thread-1] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] 01:56:50,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:56:50,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:50,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-26_01-56-50.log] [testng] 01:56:50,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19c78f9a - End of configuration. [testng] [2024-11-26 01:56:53,716] [pool-1-thread-12] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 01:56:53,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:56:53,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:53,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-26_01-56-53.log] [testng] 01:56:53,718 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6caedf5b - End of configuration. [testng] [2024-11-26 01:56:56,346] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 01:56:56,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:56:56,346 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:56,347 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-26_01-56-56.log] [testng] 01:56:56,347 |-INFO in ch.qos.logback.core.sift.SiftProcessor@e03a26a - End of configuration. [testng] [2024-11-26 01:56:59,050] [pool-1-thread-10] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] 01:56:59,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:56:59,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:56:59,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-26_01-56-59.log] [testng] 01:56:59,051 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8f2e4b3 - End of configuration. [testng] [2024-11-26 01:57:01,524] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 01:57:01,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:57:01,524 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:01,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-26_01-57-01.log] [testng] 01:57:01,525 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4a830a84 - End of configuration. [testng] [2024-11-26 01:57:04,119] [pool-1-thread-8] Initializing /data/samples/sample-extended.fli: [testng] 01:57:04,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:57:04,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:04,120 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-26_01-57-04.log] [testng] 01:57:04,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8d43452 - End of configuration. [testng] [2024-11-26 01:57:06,645] [pool-1-thread-7] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 01:57:06,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:57:06,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:06,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-26_01-57-06.log] [testng] 01:57:06,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fc79eec - End of configuration. [testng] [2024-11-26 01:57:09,525] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 01:57:09,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:57:09,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:09,526 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-26_01-57-09.log] [testng] 01:57:09,526 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60ad7c8f - End of configuration. [testng] [2024-11-26 01:57:12,164] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] 01:57:12,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:57:12,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:12,165 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-26_01-57-12.log] [testng] 01:57:12,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@712bf5d7 - End of configuration. [testng] [2024-11-26 01:57:15,278] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] 01:57:15,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:57:15,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:15,279 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-26_01-57-15.log] [testng] 01:57:15,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@28e5f74f - End of configuration. [testng] [2024-11-26 01:57:18,780] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 01:57:18,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:57:18,781 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:18,781 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-26_01-57-18.log] [testng] 01:57:18,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ae94a4e - End of configuration. [testng] [2024-11-26 01:57:22,216] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 01:57:22,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:57:22,217 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:57:22,217 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-26_01-57-22.log] [testng] 01:57:22,218 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f7ba0e5 - End of configuration. [testng] [2024-11-26 01:57:54,207] [pool-1-thread-7] Initializing /data/jean-marie/IMG_4935.JPG: [testng] [2024-11-26 01:57:55,417] [pool-1-thread-12] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] [2024-11-26 01:57:59,511] [pool-1-thread-3] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] [2024-11-26 01:58:02,034] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2024-11-26 01:58:05,927] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] [2024-11-26 01:58:08,813] [pool-1-thread-2] Initializing /data/samples/reference-extended.fli: [testng] [2024-11-26 01:58:11,729] [pool-1-thread-11] Initializing /data/jean-marie/IMG_4936.JPG: [testng] [2024-11-26 01:58:12,809] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-11-26 01:58:15,815] [pool-1-thread-1] Initializing /data/samples/lifetime-simple.fli: [testng] [2024-11-26 01:58:19,944] [pool-1-thread-9] Initializing /data/samples/sample-simple.fli: [testng] [2024-11-26 01:58:23,436] [pool-1-thread-5] Initializing /data/samples/lifetime-extended.fli: [testng] [2024-11-26 01:58:27,481] [pool-1-thread-4] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] [2024-11-26 01:58:53,388] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-11-26 01:58:56,168] [pool-1-thread-1] Initializing /data/samples/reference-simple.fli: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1378, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 57 seconds Finished: SUCCESS