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Started by upstream project "BIOFORMATS-test-repo" build number 391 originally caused by: Started by upstream project "Trigger" build number 415 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/jenkins7957553129096123837.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61831_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] 04:04:19,388 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 04:04:19,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 04:04:19,389 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:04:19,390 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 04:04:19,390 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 04:04:19,390 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 04:04:19,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 04:04:19,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:04:19,391 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 04:04:19,392 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 04:04:19,392 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 04:04:19,392 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 04:04:19,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 04:04:19,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 04:04:19,579 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 04:04:19,580 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 04:04:19,585 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 04:04:19,585 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 04:04:19,585 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 04:04:19,586 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 04:04:19,586 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 04:04:19,586 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 04:04:19,587 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 196 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-26 04:04:19,596] [main] java.version = 17.0.2 [testng] 04:04:19,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 04:04:19,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:04:19,640 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-26_04-04-19.log] [testng] 04:04:19,641 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-26 04:04:19,643] [main] testng.directory = /data [testng] [2025-03-26 04:04:19,643] [main] testng.configDirectory = /config [testng] [2025-03-26 04:04:19,652] [main] testng.multiplier = 1.0 [testng] [2025-03-26 04:04:19,652] [main] testng.in-memory = false [testng] [2025-03-26 04:04:19,653] [main] testng.allow-missing = false [testng] [2025-03-26 04:04:19,653] [main] user.language = en [testng] [2025-03-26 04:04:19,653] [main] user.country = ${user.country} [testng] [2025-03-26 04:04:19,653] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-26 04:09:18,516] [main] ---------------------------------------- [testng] [2025-03-26 04:09:18,516] [main] Total files: 28 [testng] [2025-03-26 04:09:18,516] [main] Scan time: 298.863 s (10673 ms/file) [testng] [2025-03-26 04:09:18,516] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-26 04:36:48,771] [pool-1-thread-1] Initializing /data/samples/sample-extended.fli: [testng] 04:36:48,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 04:36:48,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:36:48,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-26_04-36-48.log] [testng] 04:36:48,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@40ff61f1 - End of configuration. [testng] [2025-03-26 04:37:41,342] [pool-1-thread-12] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] 04:37:41,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 04:37:41,342 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:37:41,343 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-26_04-37-41.log] [testng] 04:37:41,343 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ea13371 - End of configuration. [testng] [2025-03-26 04:38:18,602] [pool-1-thread-11] Initializing /data/jean-marie/IMG_4936.JPG: [testng] 04:38:18,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 04:38:18,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:38:18,602 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-26_04-38-18.log] [testng] 04:38:18,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2936bfb4 - End of configuration. [testng] [2025-03-26 04:38:36,489] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 04:38:36,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 04:38:36,489 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:38:36,490 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-26_04-38-36.log] [testng] 04:38:36,490 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f0bb82a - End of configuration. [testng] [2025-03-26 04:39:23,801] [pool-1-thread-9] Initializing /data/samples/sample-simple.fli: [testng] 04:39:23,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 04:39:23,801 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:39:23,802 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-26_04-39-23.log] [testng] 04:39:23,802 |-INFO in ch.qos.logback.core.sift.SiftProcessor@741fa021 - End of configuration. [testng] [2025-03-26 04:40:18,829] [pool-1-thread-8] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 04:40:18,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 04:40:18,829 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:40:18,830 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-26_04-40-18.log] [testng] 04:40:18,830 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c00701 - End of configuration. [testng] [2025-03-26 04:41:04,113] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 04:41:04,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 04:41:04,114 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:41:04,114 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-26_04-41-04.log] [testng] 04:41:04,115 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54618efd - End of configuration. [testng] [2025-03-26 04:41:53,609] [pool-1-thread-6] Initializing /data/samples/reference-extended.fli: [testng] 04:41:53,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 04:41:53,609 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:41:53,610 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-26_04-41-53.log] [testng] 04:41:53,610 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ae622ef - End of configuration. [testng] [2025-03-26 04:42:43,454] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 04:42:43,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 04:42:43,455 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:42:43,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-26_04-42-43.log] [testng] 04:42:43,456 |-INFO in ch.qos.logback.core.sift.SiftProcessor@341ebd46 - End of configuration. [testng] [2025-03-26 04:43:41,173] [pool-1-thread-4] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] 04:43:41,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 04:43:41,173 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:43:41,174 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-26_04-43-41.log] [testng] 04:43:41,174 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22339ccb - End of configuration. [testng] [2025-03-26 04:44:25,439] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 04:44:25,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 04:44:25,439 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:44:25,440 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-26_04-44-25.log] [testng] 04:44:25,440 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6f035961 - End of configuration. [testng] [2025-03-26 04:45:12,355] [pool-1-thread-2] Initializing /data/jean-marie/IMG_4935.JPG: [testng] 04:45:12,355 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 04:45:12,356 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 04:45:12,356 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-26_04-45-12.log] [testng] 04:45:12,356 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5da37080 - End of configuration. [testng] [2025-03-26 04:52:12,904] [pool-1-thread-8] Initializing /data/samples/lifetime-extended.fli: [testng] [2025-03-26 04:53:03,445] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] [2025-03-26 04:53:59,404] [pool-1-thread-12] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] [2025-03-26 04:54:38,555] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2025-03-26 04:55:29,848] [pool-1-thread-7] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] [2025-03-26 04:56:20,558] [pool-1-thread-9] Initializing /data/samples/reference-simple.fli: [testng] [2025-03-26 04:57:13,620] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2025-03-26 04:57:59,071] [pool-1-thread-6] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] [2025-03-26 04:58:42,942] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2025-03-26 04:59:12,770] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2025-03-26 04:59:53,672] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2025-03-26 05:00:28,138] [pool-1-thread-2] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] [2025-03-26 05:04:52,879] [pool-1-thread-6] Initializing /data/samples/lifetime-simple.fli: [testng] [2025-03-26 05:05:19,265] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1378, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 65 minutes 36 seconds Finished: SUCCESS