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Started by upstream project "BIOFORMATS-test-repo" build number 101 originally caused by: Started by upstream project "Trigger" build number 112 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/jenkins9695315480403412025.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_15594_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] 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] 01:26:47,607 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:26:47,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:26:47,609 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:47,610 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:26:47,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:26:47,610 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:26:47,611 |-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] 01:26:47,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:47,611 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:26:47,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:26:47,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:26:47,612 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:26:47,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:26:47,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:26:47,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:26:47,797 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:26:47,802 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:26:47,803 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:26:47,803 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:26:47,803 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:26:47,803 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:26:47,804 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:26:47,804 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 193 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-06-23 01:26:47,813] [main] java.version = 17.0.2 [testng] 01:26:47,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:26:47,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:47,858 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-06-23_01-26-47.log] [testng] 01:26:47,859 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-06-23 01:26:47,861] [main] testng.directory = /data [testng] [2024-06-23 01:26:47,862] [main] testng.configDirectory = /config [testng] [2024-06-23 01:26:47,871] [main] testng.multiplier = 1.0 [testng] [2024-06-23 01:26:47,871] [main] testng.in-memory = false [testng] [2024-06-23 01:26:47,871] [main] testng.allow-missing = false [testng] [2024-06-23 01:26:47,872] [main] user.language = en [testng] [2024-06-23 01:26:47,872] [main] user.country = ${user.country} [testng] [2024-06-23 01:26:47,872] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-06-23 01:26:48,610] [main] ---------------------------------------- [testng] [2024-06-23 01:26:48,610] [main] Total files: 28 [testng] [2024-06-23 01:26:48,611] [main] Scan time: 0.738 s (26 ms/file) [testng] [2024-06-23 01:26:48,611] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-06-23 01:26:51,389] [pool-1-thread-1] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] 01:26:51,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:26:51,389 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,391 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-06-23_01-26-51.log] [testng] 01:26:51,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48c1a588 - End of configuration. [testng] [2024-06-23 01:26:51,471] [pool-1-thread-12] Initializing /data/samples/reference-simple.fli: [testng] 01:26:51,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:26:51,472 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,473 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-06-23_01-26-51.log] [testng] 01:26:51,473 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54f7153b - End of configuration. [testng] [2024-06-23 01:26:51,496] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 01:26:51,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:26:51,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-06-23_01-26-51.log] [testng] 01:26:51,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d77bd67 - End of configuration. [testng] [2024-06-23 01:26:51,532] [pool-1-thread-10] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] 01:26:51,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:26:51,532 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,533 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-06-23_01-26-51.log] [testng] 01:26:51,533 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f5b5ba - End of configuration. [testng] [2024-06-23 01:26:51,565] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] 01:26:51,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:26:51,565 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,566 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-06-23_01-26-51.log] [testng] 01:26:51,567 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77a97b46 - End of configuration. [testng] [2024-06-23 01:26:51,596] [pool-1-thread-8] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] 01:26:51,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:26:51,597 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,597 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-06-23_01-26-51.log] [testng] 01:26:51,598 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22797d27 - End of configuration. [testng] [2024-06-23 01:26:51,620] [pool-1-thread-7] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 01:26:51,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:26:51,620 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,621 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-06-23_01-26-51.log] [testng] 01:26:51,622 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e06a764 - End of configuration. [testng] [2024-06-23 01:26:51,653] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] 01:26:51,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:26:51,653 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-06-23_01-26-51.log] [testng] 01:26:51,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@210b5e37 - End of configuration. [testng] [2024-06-23 01:26:51,687] [pool-1-thread-5] Initializing /data/samples/sample-simple.fli: [testng] 01:26:51,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:26:51,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-06-23_01-26-51.log] [testng] 01:26:51,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b960ddb - End of configuration. [testng] [2024-06-23 01:26:51,699] [pool-1-thread-4] Initializing /data/jean-marie/IMG_4935.JPG: [testng] 01:26:51,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:26:51,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:51,700 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-06-23_01-26-51.log] [testng] 01:26:51,701 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4ca64c0f - End of configuration. [testng] [2024-06-23 01:26:52,008] [pool-1-thread-3] Initializing /data/samples/reference-extended.fli: [testng] 01:26:52,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:26:52,008 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:52,009 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-06-23_01-26-52.log] [testng] 01:26:52,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5193aac4 - End of configuration. [testng] [2024-06-23 01:26:52,041] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] 01:26:52,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:26:52,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:26:52,043 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-06-23_01-26-52.log] [testng] 01:26:52,043 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78b425e2 - End of configuration. [testng] [2024-06-23 01:26:53,143] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2024-06-23 01:26:53,183] [pool-1-thread-5] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] [2024-06-23 01:26:53,205] [pool-1-thread-3] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] [2024-06-23 01:26:53,234] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2024-06-23 01:26:53,525] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-06-23 01:26:53,559] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [2024-06-23 01:26:54,063] [pool-1-thread-10] Initializing /data/jean-marie/IMG_4936.JPG: [testng] [2024-06-23 01:26:54,408] [pool-1-thread-1] Initializing /data/samples/lifetime-simple.fli: [testng] [2024-06-23 01:26:54,417] [pool-1-thread-2] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] [2024-06-23 01:26:54,435] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-06-23 01:26:54,487] [pool-1-thread-9] Initializing /data/samples/lifetime-extended.fli: [testng] [2024-06-23 01:26:54,526] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-06-23 01:26:54,567] [pool-1-thread-12] Initializing /data/samples/sample-extended.fli: [testng] [2024-06-23 01:26:54,667] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1378, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 17 seconds Finished: SUCCESS