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Started by upstream project "BIOFORMATS-test-repo" build number 209 originally caused by: Started by upstream project "Trigger" build number 235 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/jenkins17073921395826700814.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_33149_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] 01:37:52,060 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:37:52,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - No custom configurators were discovered as a service. [testng] 01:37:52,061 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:37:52,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:37:52,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:37:52,063 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:37:52,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:37:52,063 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:37:52,064 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:37:52,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:37:52,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:37:52,064 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:37:52,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:37:52,289 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:37:52,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:37:52,317 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:37:52,325 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:37:52,326 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:37:52,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:37:52,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:37:52,326 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@1ddf84b8 - End of configuration. [testng] 01:37:52,327 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@5e82df6a - Registering current configuration as safe fallback point [testng] 01:37:52,327 |-INFO in ch.qos.logback.classic.util.ContextInitializer@197d671 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 263 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-04 01:37:52,337] [main] java.version = 1.8.0_342 [testng] 01:37:52,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:37:52,341 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:37:52,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-04_01-37-52.log] [testng] 01:37:52,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36fc695d - End of configuration. [testng] [2024-10-04 01:37:52,389] [main] testng.directory = /data [testng] [2024-10-04 01:37:52,390] [main] testng.configDirectory = /config [testng] [2024-10-04 01:37:52,402] [main] testng.multiplier = 1.0 [testng] [2024-10-04 01:37:52,402] [main] testng.in-memory = false [testng] [2024-10-04 01:37:52,402] [main] testng.allow-missing = false [testng] [2024-10-04 01:37:52,402] [main] user.language = en [testng] [2024-10-04 01:37:52,402] [main] user.country = ${user.country} [testng] [2024-10-04 01:37:52,402] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-10-04 01:37:54,180] [main] ---------------------------------------- [testng] [2024-10-04 01:37:54,180] [main] Total files: 28 [testng] [2024-10-04 01:37:54,180] [main] Scan time: 1.777 s (63 ms/file) [testng] [2024-10-04 01:37:54,180] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-04 01:38:00,045] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] 01:38:00,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:38:00,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-04_01-38-00.log] [testng] 01:38:00,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a1d2e3 - End of configuration. [testng] [2024-10-04 01:38:00,252] [pool-1-thread-12] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] 01:38:00,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:38:00,253 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-04_01-38-00.log] [testng] 01:38:00,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57bffd0e - End of configuration. [testng] [2024-10-04 01:38:00,452] [pool-1-thread-11] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] 01:38:00,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:38:00,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,453 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-04_01-38-00.log] [testng] 01:38:00,454 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ddc1e72 - End of configuration. [testng] [2024-10-04 01:38:00,517] [pool-1-thread-10] Initializing /data/samples/lifetime-simple.fli: [testng] 01:38:00,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:38:00,518 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,519 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-04_01-38-00.log] [testng] 01:38:00,519 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a49d4dc - End of configuration. [testng] [2024-10-04 01:38:00,689] [pool-1-thread-9] Initializing /data/samples/reference-simple.fli: [testng] 01:38:00,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:38:00,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-04_01-38-00.log] [testng] 01:38:00,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48b9580b - End of configuration. [testng] [2024-10-04 01:38:00,865] [pool-1-thread-8] Initializing /data/samples/sample-simple.fli: [testng] 01:38:00,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:38:00,865 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,866 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-04_01-38-00.log] [testng] 01:38:00,866 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f8a45ac - End of configuration. [testng] [2024-10-04 01:38:00,986] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] 01:38:00,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:38:00,986 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:00,987 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-04_01-38-00.log] [testng] 01:38:00,988 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68bb9f81 - End of configuration. [testng] [2024-10-04 01:38:01,090] [pool-1-thread-6] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] 01:38:01,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:38:01,091 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:01,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-04_01-38-01.log] [testng] 01:38:01,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2fb99b0b - End of configuration. [testng] [2024-10-04 01:38:01,162] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 01:38:01,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:38:01,162 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:01,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-04_01-38-01.log] [testng] 01:38:01,179 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2e799487 - End of configuration. [testng] [2024-10-04 01:38:01,308] [pool-1-thread-4] Initializing /data/jean-marie/IMG_4935.JPG: [testng] 01:38:01,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:38:01,308 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:01,308 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-04_01-38-01.log] [testng] 01:38:01,309 |-INFO in ch.qos.logback.core.sift.SiftProcessor@10b83541 - End of configuration. [testng] [2024-10-04 01:38:01,670] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 01:38:01,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:38:01,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:01,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-04_01-38-01.log] [testng] 01:38:01,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e39d3b1 - End of configuration. [testng] [2024-10-04 01:38:01,794] [pool-1-thread-2] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] 01:38:01,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:38:01,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:38:01,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-04_01-38-01.log] [testng] 01:38:01,796 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6cf9d03f - End of configuration. [testng] [2024-10-04 01:38:04,444] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-10-04 01:38:04,518] [pool-1-thread-8] Initializing /data/jean-marie/IMG_4936.JPG: [testng] [2024-10-04 01:38:04,892] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-10-04 01:38:05,047] [pool-1-thread-5] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] [2024-10-04 01:38:05,269] [pool-1-thread-1] Initializing /data/samples/sample-extended.fli: [testng] [2024-10-04 01:38:05,936] [pool-1-thread-6] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] [2024-10-04 01:38:06,664] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [2024-10-04 01:38:06,727] [pool-1-thread-3] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] [2024-10-04 01:38:06,880] [pool-1-thread-11] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] [2024-10-04 01:38:07,836] [pool-1-thread-1] Initializing /data/samples/reference-extended.fli: [testng] [2024-10-04 01:38:08,040] [pool-1-thread-9] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2024-10-04 01:38:08,466] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2024-10-04 01:38:08,641] [pool-1-thread-6] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] [2024-10-04 01:38:08,739] [pool-1-thread-5] Initializing /data/samples/lifetime-extended.fli: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1378, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 28 seconds Finished: SUCCESS