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Started by upstream project "BIOFORMATS-test-repo" build number 362 originally caused by: Started by upstream project "Trigger" build number 388 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins1007161767270512626.sh + '[' li-flim = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57674_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] 00:44:15,446 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:44:15,448 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:44:15,448 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:44:15,449 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:44:15,449 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:44:15,449 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:44:15,450 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:44:15,450 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:44:15,450 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:44:15,451 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:44:15,451 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:44:15,451 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:44:15,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:44:15,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:44:15,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:44:15,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:44:15,646 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:44:15,647 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:44:15,647 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:44:15,647 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:44:15,647 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:44:15,648 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:44:15,649 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 199 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-02 00:44:15,658] [main] java.version = 17.0.2 [testng] 00:44:15,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:44:15,661 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:15,702 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-02_00-44-15.log] [testng] 00:44:15,703 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-02 00:44:15,705] [main] testng.directory = /data [testng] [2025-03-02 00:44:15,706] [main] testng.configDirectory = /config [testng] [2025-03-02 00:44:15,715] [main] testng.multiplier = 1.0 [testng] [2025-03-02 00:44:15,715] [main] testng.in-memory = false [testng] [2025-03-02 00:44:15,716] [main] testng.allow-missing = false [testng] [2025-03-02 00:44:15,716] [main] user.language = en [testng] [2025-03-02 00:44:15,716] [main] user.country = ${user.country} [testng] [2025-03-02 00:44:15,716] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-02 00:44:17,967] [main] ---------------------------------------- [testng] [2025-03-02 00:44:17,967] [main] Total files: 28 [testng] [2025-03-02 00:44:17,967] [main] Scan time: 2.251 s (80 ms/file) [testng] [2025-03-02 00:44:17,967] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 26 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-02 00:44:24,325] [pool-1-thread-1] Initializing /data/samples/sample-extended.fli: [testng] 00:44:24,328 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:44:24,329 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:24,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-02_00-44-24.log] [testng] 00:44:24,336 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4121f311 - End of configuration. [testng] [2025-03-02 00:44:24,552] [pool-1-thread-12] Initializing /data/LambertInstruments/cp70-siso_Lambert HS1000_1875-ST-250(lsb).fli: [testng] 00:44:24,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:44:24,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:24,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-02_00-44-24.log] [testng] 00:44:24,554 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f93e1fa - End of configuration. [testng] [2025-03-02 00:44:24,659] [pool-1-thread-11] Initializing /data/jean-marie/IMG_4936.JPG: [testng] 00:44:24,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:44:24,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:24,660 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-02_00-44-24.log] [testng] 00:44:24,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@232af398 - End of configuration. [testng] [2025-03-02 00:44:25,016] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/lif_A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 00:44:25,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:44:25,016 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,017 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-02_00-44-25.log] [testng] 00:44:25,017 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56c65529 - End of configuration. [testng] [2025-03-02 00:44:25,101] [pool-1-thread-9] Initializing /data/samples/sample-simple.fli: [testng] 00:44:25,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:44:25,101 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,102 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-02_00-44-25.log] [testng] 00:44:25,103 |-INFO in ch.qos.logback.core.sift.SiftProcessor@217aa209 - End of configuration. [testng] [2025-03-02 00:44:25,261] [pool-1-thread-8] Initializing /data/LambertInstruments/LambertInstruments-fli-2/15-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] 00:44:25,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:44:25,262 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,262 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-02_00-44-25.log] [testng] 00:44:25,263 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6af89944 - End of configuration. [testng] [2025-03-02 00:44:25,430] [pool-1-thread-7] Initializing /data/jean-marie/Flimdata/A Sample CFP-and-CFPYFP-cells-CFPbpFILTER.fli: [testng] 00:44:25,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:44:25,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-02_00-44-25.log] [testng] 00:44:25,432 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d6abcab - End of configuration. [testng] [2025-03-02 00:44:25,619] [pool-1-thread-6] Initializing /data/samples/reference-extended.fli: [testng] 00:44:25,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:44:25,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-02_00-44-25.log] [testng] 00:44:25,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7081c9a0 - End of configuration. [testng] [2025-03-02 00:44:25,802] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/lif_C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] 00:44:25,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:44:25,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,803 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-02_00-44-25.log] [testng] 00:44:25,804 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21d944d - End of configuration. [testng] [2025-03-02 00:44:25,989] [pool-1-thread-4] Initializing /data/rharkes/2018-11-28_10.04.10_sample_Rhodamine6G.fli: [testng] 00:44:25,989 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:44:25,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:25,990 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-02_00-44-25.log] [testng] 00:44:25,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22cb2169 - End of configuration. [testng] [2025-03-02 00:44:26,088] [pool-1-thread-3] Initializing /data/jean-marie/Flimdata/C Reference fluorescein4ns-CFPbpFILTER.fli: [testng] 00:44:26,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:44:26,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:26,091 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-02_00-44-26.log] [testng] 00:44:26,092 |-INFO in ch.qos.logback.core.sift.SiftProcessor@314e1183 - End of configuration. [testng] [2025-03-02 00:44:26,219] [pool-1-thread-2] Initializing /data/jean-marie/IMG_4935.JPG: [testng] 00:44:26,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:44:26,219 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:44:26,220 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-02_00-44-26.log] [testng] 00:44:26,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e5acffa - End of configuration. [testng] [2025-03-02 00:44:28,987] [pool-1-thread-9] Initializing /data/samples/lifetime-extended.fli: [testng] [2025-03-02 00:44:29,149] [pool-1-thread-6] Initializing /data/jean-marie/Flimdata/E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2025-03-02 00:44:29,219] [pool-1-thread-1] Initializing /data/jean-marie/Flimdata/E Reference fluorescein4ns-CSU22.fli: [testng] [2025-03-02 00:44:29,419] [pool-1-thread-10] Initializing /data/jean-marie/Flimdata/C Sample CFP-and-CFPYFP-cells-CFPbpFILTER-slow timelapse.fli: [testng] [2025-03-02 00:44:29,696] [pool-1-thread-5] Initializing /data/LambertInstruments/LambertInstruments-fli-2/16-8bit_CameraSimulator_LI-Camera-Simulator.fli: [testng] [2025-03-02 00:44:29,977] [pool-1-thread-8] Initializing /data/jean-marie/Flimdata/lif_D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2025-03-02 00:44:30,535] [pool-1-thread-4] Initializing /data/samples/reference-simple.fli: [testng] [2025-03-02 00:44:30,605] [pool-1-thread-12] Initializing /data/jean-marie/Flimdata/lif_E Sample Typical-Dicot-Root-Zserie-CSU22.fli: [testng] [2025-03-02 00:44:30,713] [pool-1-thread-7] Initializing /data/LambertInstruments/cp70-euresys_Lambert HS1000_1875-ST-250(msb).fli: [testng] [2025-03-02 00:44:30,817] [pool-1-thread-3] Initializing /data/qian/vxl-mbad-737-1um-01687.fli: [testng] [2025-03-02 00:44:31,306] [pool-1-thread-9] Initializing /data/qa-17164/ExampleFile - LiFlimReader fix ExposureTime .fli: [testng] [2025-03-02 00:44:31,983] [pool-1-thread-5] Initializing /data/jean-marie/Flimdata/D Sample CFPYFP-cells-CFPbpFILTER-multifreq.fli: [testng] [2025-03-02 00:44:32,096] [pool-1-thread-8] Initializing /data/samples/lifetime-simple.fli: [testng] [2025-03-02 00:44:32,175] [pool-1-thread-4] 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: 34 seconds Finished: SUCCESS