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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@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins2347071397486010191.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_46779_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 test-automated: [testng] File leak detector installed [testng] 00:52:15,287 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:52:15,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:52:15,289 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:52:15,290 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:52:15,290 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:52:15,290 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:52:15,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:52:15,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:52:15,291 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:52:15,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:52:15,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:52:15,292 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:52:15,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:52:15,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:52:15,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:52:15,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:52:15,570 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:52:15,571 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:52:15,571 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:52:15,572 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:52:15,572 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:52:15,573 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:52:15,573 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 282 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-20 00:52:15,583] [main] java.version = 1.8.0_342 [testng] 00:52:15,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:52:15,587 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:15,633 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-20_00-52-15.log] [testng] 00:52:15,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-20 00:52:15,637] [main] testng.directory = /data [testng] [2024-12-20 00:52:15,638] [main] testng.configDirectory = /config [testng] [2024-12-20 00:52:15,650] [main] testng.multiplier = 1.0 [testng] [2024-12-20 00:52:15,651] [main] testng.in-memory = false [testng] [2024-12-20 00:52:15,651] [main] testng.allow-missing = false [testng] [2024-12-20 00:52:15,651] [main] user.language = en [testng] [2024-12-20 00:52:15,651] [main] user.country = ${user.country} [testng] [2024-12-20 00:52:15,651] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-20 00:52:20,440] [main] ---------------------------------------- [testng] [2024-12-20 00:52:20,440] [main] Total files: 28 [testng] [2024-12-20 00:52:20,440] [main] Scan time: 4.789 s (171 ms/file) [testng] [2024-12-20 00:52:20,441] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-20 00:52:33,653] [pool-1-thread-1] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] 00:52:33,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:52:33,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:33,656 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-20_00-52-33.log] [testng] 00:52:33,656 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30b24e2e - End of configuration. [testng] [2024-12-20 00:52:34,021] [pool-1-thread-12] Initializing /data/samples/reference-simple.fli: [testng] 00:52:34,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:52:34,021 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:34,022 |-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_00-52-34.log] [testng] 00:52:34,022 |-INFO in ch.qos.logback.core.sift.SiftProcessor@89e2763 - End of configuration. [testng] [2024-12-20 00:52:34,590] [pool-1-thread-11] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 00:52:34,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:52:34,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:34,591 |-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_00-52-34.log] [testng] 00:52:34,591 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4cf550c - End of configuration. [testng] [2024-12-20 00:52:35,180] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] 00:52:35,180 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:52:35,181 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:35,181 |-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_00-52-35.log] [testng] 00:52:35,181 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57bffd0e - End of configuration. [testng] [2024-12-20 00:52:35,733] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] 00:52:35,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:52:35,733 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:35,734 |-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_00-52-35.log] [testng] 00:52:35,734 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7067f9cd - End of configuration. [testng] [2024-12-20 00:52:36,199] [pool-1-thread-8] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 00:52:36,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:52:36,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:36,200 |-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_00-52-36.log] [testng] 00:52:36,200 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4189e938 - End of configuration. [testng] [2024-12-20 00:52:36,695] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 00:52:36,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:52:36,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:36,696 |-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_00-52-36.log] [testng] 00:52:36,696 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18de830d - End of configuration. [testng] [2024-12-20 00:52:37,445] [pool-1-thread-6] Initializing /data/jean-marie/IMG_4936.JPG: [testng] 00:52:37,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:52:37,446 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:37,446 |-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_00-52-37.log] [testng] 00:52:37,446 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30b9efb4 - End of configuration. [testng] [2024-12-20 00:52:37,871] [pool-1-thread-5] Initializing /data/samples/lifetime-extended.fli: [testng] 00:52:37,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:52:37,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:37,872 |-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_00-52-37.log] [testng] 00:52:37,873 |-INFO in ch.qos.logback.core.sift.SiftProcessor@170ffe5b - End of configuration. [testng] [2024-12-20 00:52:38,295] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] 00:52:38,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:52:38,296 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:38,296 |-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_00-52-38.log] [testng] 00:52:38,296 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75c44bda - End of configuration. [testng] [2024-12-20 00:52:38,977] [pool-1-thread-3] Initializing /data/jean-marie/IMG_4935.JPG: [testng] 00:52:38,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:52:38,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:38,979 |-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_00-52-38.log] [testng] 00:52:38,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62cd3836 - End of configuration. [testng] [2024-12-20 00:52:39,474] [pool-1-thread-2] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] 00:52:39,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:52:39,474 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:39,475 |-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_00-52-39.log] [testng] 00:52:39,475 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f38fec0 - End of configuration. [testng] [2024-12-20 00:52:45,669] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-12-20 00:52:45,971] [pool-1-thread-5] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] [2024-12-20 00:52:46,294] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2024-12-20 00:52:46,635] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [2024-12-20 00:52:46,986] [pool-1-thread-8] Initializing /data/samples/lifetime-simple.fli: [testng] [2024-12-20 00:52:47,244] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-12-20 00:52:47,500] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [2024-12-20 00:52:47,771] [pool-1-thread-4] Initializing /data/samples/reference-extended.fli: [testng] [2024-12-20 00:52:48,018] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-12-20 00:52:50,868] [pool-1-thread-7] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] [2024-12-20 00:52:52,153] [pool-1-thread-8] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] [2024-12-20 00:52:52,750] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2024-12-20 00:52:53,281] [pool-1-thread-6] Initializing /data/samples/sample-extended.fli: [testng] [2024-12-20 00:52:53,688] [pool-1-thread-2] Initializing /data/samples/sample-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: 49 seconds Finished: SUCCESS