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Started by upstream project "BIOFORMATS-test-repo" build number 8 originally caused by: Started by upstream project "Trigger" build number 11 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins680030586688617950.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_1159_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] 00:30:08,164 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:30:08,166 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 00:30:08,166 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:08,167 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:30:08,167 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:30:08,168 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:30:08,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:30:08,168 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:08,169 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:30:08,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:30:08,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:30:08,169 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:30:08,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:30:08,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:30:08,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:30:08,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:30:08,540 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:30:08,541 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:30:08,541 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:30:08,541 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:30:08,541 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 00:30:08,542 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 00:30:08,543 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 374 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-22 00:30:08,555] [main] java.version = 1.8.0_342 [testng] 00:30:08,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:30:08,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:08,630 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-22_00-30-08.log] [testng] 00:30:08,632 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-03-22 00:30:08,634] [main] testng.directory = /data [testng] [2024-03-22 00:30:08,634] [main] testng.configDirectory = /config [testng] [2024-03-22 00:30:08,650] [main] testng.multiplier = 1.0 [testng] [2024-03-22 00:30:08,650] [main] testng.in-memory = false [testng] [2024-03-22 00:30:08,651] [main] testng.allow-missing = false [testng] [2024-03-22 00:30:08,651] [main] user.language = en [testng] [2024-03-22 00:30:08,651] [main] user.country = ${user.country} [testng] [2024-03-22 00:30:08,651] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-03-22 00:30:10,245] [main] ---------------------------------------- [testng] [2024-03-22 00:30:10,246] [main] Total files: 28 [testng] [2024-03-22 00:30:10,246] [main] Scan time: 1.594 s (56 ms/file) [testng] [2024-03-22 00:30:10,246] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-22 00:30:18,702] [pool-1-thread-1] Initializing /data/samples/reference-extended.fli: [testng] 00:30:18,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:30:18,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:18,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-22_00-30-18.log] [testng] 00:30:18,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bd0a175 - End of configuration. [testng] [2024-03-22 00:30:18,826] [pool-1-thread-12] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] 00:30:18,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:30:18,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:18,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-22_00-30-18.log] [testng] 00:30:18,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ae27a4 - End of configuration. [testng] [2024-03-22 00:30:18,973] [pool-1-thread-11] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] 00:30:18,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:30:18,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:18,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-22_00-30-18.log] [testng] 00:30:18,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10d71f49 - End of configuration. [testng] [2024-03-22 00:30:19,027] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 00:30:19,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:30:19,027 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,028 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-22_00-30-19.log] [testng] 00:30:19,029 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cf367dc - End of configuration. [testng] [2024-03-22 00:30:19,165] [pool-1-thread-9] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 00:30:19,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:30:19,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-22_00-30-19.log] [testng] 00:30:19,167 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59389b5f - End of configuration. [testng] [2024-03-22 00:30:19,308] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 00:30:19,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:30:19,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,309 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-22_00-30-19.log] [testng] 00:30:19,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4077b502 - End of configuration. [testng] [2024-03-22 00:30:19,434] [pool-1-thread-7] Initializing /data/samples/lifetime-extended.fli: [testng] 00:30:19,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:30:19,434 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-22_00-30-19.log] [testng] 00:30:19,435 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9c8665 - End of configuration. [testng] [2024-03-22 00:30:19,478] [pool-1-thread-6] Initializing /data/samples/sample-extended.fli: [testng] 00:30:19,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:30:19,478 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,479 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-22_00-30-19.log] [testng] 00:30:19,479 |-INFO in ch.qos.logback.core.sift.SiftProcessor@766d4ad0 - End of configuration. [testng] [2024-03-22 00:30:19,554] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] 00:30:19,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:30:19,555 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,556 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-22_00-30-19.log] [testng] 00:30:19,556 |-INFO in ch.qos.logback.core.sift.SiftProcessor@290f809a - End of configuration. [testng] [2024-03-22 00:30:19,642] [pool-1-thread-4] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] 00:30:19,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:30:19,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,644 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-22_00-30-19.log] [testng] 00:30:19,644 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f0b3ced - End of configuration. [testng] [2024-03-22 00:30:19,690] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 00:30:19,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:30:19,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-22_00-30-19.log] [testng] 00:30:19,691 |-INFO in ch.qos.logback.core.sift.SiftProcessor@af0cfd1 - End of configuration. [testng] [2024-03-22 00:30:19,743] [pool-1-thread-2] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] 00:30:19,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:30:19,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:30:19,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-22_00-30-19.log] [testng] 00:30:19,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@735e9da3 - End of configuration. [testng] [2024-03-22 00:30:21,512] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-03-22 00:30:21,628] [pool-1-thread-1] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] [2024-03-22 00:30:21,943] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-03-22 00:30:22,117] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2024-03-22 00:30:22,150] [pool-1-thread-6] Initializing /data/samples/reference-simple.fli: [testng] [2024-03-22 00:30:22,391] [pool-1-thread-9] Initializing /data/samples/sample-simple.fli: [testng] [2024-03-22 00:30:22,508] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2024-03-22 00:30:22,681] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-03-22 00:30:22,712] [pool-1-thread-4] Initializing /data/jean-marie/IMG_4935.JPG: [testng] [2024-03-22 00:30:23,652] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] [2024-03-22 00:30:23,710] [pool-1-thread-10] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] [2024-03-22 00:30:23,786] [pool-1-thread-6] Initializing /data/samples/lifetime-simple.fli: [testng] [2024-03-22 00:30:23,817] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [2024-03-22 00:30:24,312] [pool-1-thread-6] Initializing /data/jean-marie/IMG_4936.JPG: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1378, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 32 seconds Finished: SUCCESS