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Started by upstream project "BIOFORMATS-test-repo" build number 241 originally caused by: Started by upstream project "Trigger" build number 266 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/jenkins9934435683203009261.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37881_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] 00:43:15,198 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:43:15,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 00:43:15,200 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:43:15,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:43:15,201 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:43:15,201 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:43:15,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:43:15,201 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:43:15,202 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:43:15,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:43:15,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:43:15,202 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:43:15,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:43:15,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:43:15,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:43:15,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:43:15,478 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:43:15,478 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:43:15,478 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:43:15,479 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:43:15,479 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 00:43:15,480 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 00:43:15,480 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 278 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-01 00:43:15,491] [main] java.version = 1.8.0_342 [testng] 00:43:15,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:43:15,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:15,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-01_00-43-15.log] [testng] 00:43:15,548 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-11-01 00:43:15,550] [main] testng.directory = /data [testng] [2024-11-01 00:43:15,551] [main] testng.configDirectory = /config [testng] [2024-11-01 00:43:15,564] [main] testng.multiplier = 1.0 [testng] [2024-11-01 00:43:15,565] [main] testng.in-memory = false [testng] [2024-11-01 00:43:15,565] [main] testng.allow-missing = false [testng] [2024-11-01 00:43:15,565] [main] user.language = en [testng] [2024-11-01 00:43:15,565] [main] user.country = ${user.country} [testng] [2024-11-01 00:43:15,565] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-11-01 00:43:17,695] [main] ---------------------------------------- [testng] [2024-11-01 00:43:17,695] [main] Total files: 28 [testng] [2024-11-01 00:43:17,695] [main] Scan time: 2.13 s (76 ms/file) [testng] [2024-11-01 00:43:17,695] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-01 00:43:25,971] [pool-1-thread-1] Initializing /data/samples/lifetime-simple.fli: [testng] 00:43:25,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:43:25,973 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:25,974 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-01_00-43-25.log] [testng] 00:43:25,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57cf859a - End of configuration. [testng] [2024-11-01 00:43:26,101] [pool-1-thread-12] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] 00:43:26,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:43:26,102 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:26,103 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-01_00-43-26.log] [testng] 00:43:26,104 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6445f40e - End of configuration. [testng] [2024-11-01 00:43:26,217] [pool-1-thread-11] Initializing /data/jean-marie/IMG_4936.JPG: [testng] 00:43:26,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:43:26,218 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:26,219 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-01_00-43-26.log] [testng] 00:43:26,220 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2691547e - End of configuration. [testng] [2024-11-01 00:43:26,618] [pool-1-thread-10] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] 00:43:26,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:43:26,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:26,619 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-01_00-43-26.log] [testng] 00:43:26,619 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b584016 - End of configuration. [testng] [2024-11-01 00:43:26,975] [pool-1-thread-9] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 00:43:26,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:43:26,976 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:26,977 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-01_00-43-26.log] [testng] 00:43:26,977 |-INFO in ch.qos.logback.core.sift.SiftProcessor@408ab794 - End of configuration. [testng] [2024-11-01 00:43:27,120] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] 00:43:27,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:43:27,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:27,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-01_00-43-27.log] [testng] 00:43:27,121 |-INFO in ch.qos.logback.core.sift.SiftProcessor@298cf3e6 - End of configuration. [testng] [2024-11-01 00:43:27,284] [pool-1-thread-7] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] 00:43:27,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:43:27,284 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:27,285 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-01_00-43-27.log] [testng] 00:43:27,285 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1380039a - End of configuration. [testng] [2024-11-01 00:43:27,548] [pool-1-thread-6] Initializing /data/samples/reference-simple.fli: [testng] 00:43:27,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:43:27,548 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:27,549 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-01_00-43-27.log] [testng] 00:43:27,549 |-INFO in ch.qos.logback.core.sift.SiftProcessor@721e4ac8 - End of configuration. [testng] [2024-11-01 00:43:27,697] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 00:43:27,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:43:27,698 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:27,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-01_00-43-27.log] [testng] 00:43:27,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7dfcdceb - End of configuration. [testng] [2024-11-01 00:43:27,826] [pool-1-thread-4] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] 00:43:27,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:43:27,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:27,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-01_00-43-27.log] [testng] 00:43:27,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1015b648 - End of configuration. [testng] [2024-11-01 00:43:27,972] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 00:43:27,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:43:27,972 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:27,973 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-01_00-43-27.log] [testng] 00:43:27,974 |-INFO in ch.qos.logback.core.sift.SiftProcessor@779a6beb - End of configuration. [testng] [2024-11-01 00:43:28,136] [pool-1-thread-2] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 00:43:28,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:43:28,136 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:43:28,137 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-01_00-43-28.log] [testng] 00:43:28,138 |-INFO in ch.qos.logback.core.sift.SiftProcessor@449a8550 - End of configuration. [testng] [2024-11-01 00:43:31,705] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/A Reference fluorescein4ns-CFPbpFILTER.fli: [testng] [2024-11-01 00:43:31,816] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-11-01 00:43:32,047] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2024-11-01 00:43:32,289] [pool-1-thread-5] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] [2024-11-01 00:43:32,876] [pool-1-thread-2] Initializing /data/samples/reference-extended.fli: [testng] [2024-11-01 00:43:33,266] [pool-1-thread-9] Initializing /data/samples/sample-extended.fli: [testng] [2024-11-01 00:43:33,504] [pool-1-thread-4] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] [2024-11-01 00:43:33,665] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2024-11-01 00:43:33,774] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2024-11-01 00:43:33,977] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2024-11-01 00:43:35,647] [pool-1-thread-12] Initializing /data/samples/sample-simple.fli: [testng] [2024-11-01 00:43:35,773] [pool-1-thread-5] Initializing /data/samples/lifetime-extended.fli: [testng] [2024-11-01 00:43:35,946] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] [2024-11-01 00:43:36,048] [pool-1-thread-2] Initializing /data/jean-marie/IMG_4935.JPG: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1378, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 34 seconds Finished: SUCCESS