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Started by upstream project "BIOFORMATS-test-repo" build number 299 originally caused by: Started by upstream project "Trigger" build number 321 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins17999119117889440356.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_47290_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/merge-ci/curated/flex:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings 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] 01:04:03,397 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:04:03,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 01:04:03,399 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:04:03,400 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:04:03,400 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:04:03,401 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:04:03,401 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:04:03,401 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:04:03,401 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:04:03,402 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:04:03,402 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:04:03,403 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:04:03,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:04:03,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:04:03,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:04:03,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:04:03,596 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:04:03,596 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:04:03,596 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:04:03,597 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:04:03,597 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 01:04:03,598 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 01:04:03,598 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-26 01:04:03,607] [main] java.version = 21 [testng] 01:04:03,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:04:03,610 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:04:03,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-26_01-04-03.log] [testng] 01:04:03,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-26 01:04:03,656] [main] testng.directory = /data [testng] [2024-12-26 01:04:03,656] [main] testng.configDirectory = /config [testng] [2024-12-26 01:04:03,666] [main] testng.multiplier = 1.0 [testng] [2024-12-26 01:04:03,666] [main] testng.in-memory = false [testng] [2024-12-26 01:04:03,666] [main] testng.allow-missing = false [testng] [2024-12-26 01:04:03,666] [main] user.language = en [testng] [2024-12-26 01:04:03,666] [main] user.country = ${user.country} [testng] [2024-12-26 01:04:03,667] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-26 01:06:21,135] [main] ---------------------------------------- [testng] [2024-12-26 01:06:21,135] [main] Total files: 791 [testng] [2024-12-26 01:06:21,135] [main] Scan time: 137.468 s (173 ms/file) [testng] [2024-12-26 01:06:21,136] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-26 01:13:11,905] [pool-1-thread-1] Initializing /data/tony/015002000.tiff: [testng] 01:13:11,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:13:11,906 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:11,908 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-26_01-13-11.log] [testng] 01:13:11,908 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62aad765 - End of configuration. [testng] [2024-12-26 01:13:14,120] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 01:13:14,120 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:13:14,121 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:14,121 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-26_01-13-14.log] [testng] 01:13:14,122 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1aa3dedf - End of configuration. [testng] [2024-12-26 01:13:22,005] [pool-1-thread-11] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:13:22,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:13:22,006 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:22,008 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-26_01-13-22.log] [testng] 01:13:22,009 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bb23c7b - End of configuration. [testng] [2024-12-26 01:13:24,593] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:13:24,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:13:24,593 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:24,594 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-26_01-13-24.log] [testng] 01:13:24,594 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e93d9b7 - End of configuration. [testng] [2024-12-26 01:13:34,504] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] 01:13:34,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:13:34,504 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:34,505 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-26_01-13-34.log] [testng] 01:13:34,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349d1354 - End of configuration. [testng] [2024-12-26 01:13:35,619] [pool-1-thread-8] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:13:35,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:13:35,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:35,620 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-26_01-13-35.log] [testng] 01:13:35,620 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48da454b - End of configuration. [testng] [2024-12-26 01:13:36,739] [pool-1-thread-7] Initializing /data/tony/test1.flex: [testng] 01:13:36,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:13:36,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:36,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-26_01-13-36.log] [testng] 01:13:36,741 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7339ac33 - End of configuration. [testng] [2024-12-26 01:13:37,822] [pool-1-thread-6] Initializing /data/tony/003008000.flex: [testng] 01:13:37,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:13:37,822 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:37,823 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-26_01-13-37.log] [testng] 01:13:37,823 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46eaab39 - End of configuration. [testng] [2024-12-26 01:13:38,930] [pool-1-thread-5] Initializing /data/tony/001001000_objects.flex: [testng] 01:13:38,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:13:38,930 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:38,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-26_01-13-38.log] [testng] 01:13:38,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cc52d5d - End of configuration. [testng] [2024-12-26 01:13:40,177] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 01:13:40,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:13:40,177 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:40,178 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-26_01-13-40.log] [testng] 01:13:40,178 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b86fc93 - End of configuration. [testng] [2024-12-26 01:13:41,545] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex: [testng] 01:13:41,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:13:41,545 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:41,546 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-26_01-13-41.log] [testng] 01:13:41,546 |-INFO in ch.qos.logback.core.sift.SiftProcessor@30e2e4ed - End of configuration. [testng] [2024-12-26 01:13:42,605] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 01:13:42,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:13:42,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:13:42,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-26_01-13-42.log] [testng] 01:13:42,607 |-INFO in ch.qos.logback.core.sift.SiftProcessor@353a6f3e - End of configuration. [testng] [2024-12-26 01:13:59,034] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-26 01:14:00,513] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-12-26 01:14:01,675] [pool-1-thread-3] Initializing /data/tony/test.tiff: [testng] [2024-12-26 01:14:03,703] [pool-1-thread-7] Initializing /data/tony/003003000.tiff: [testng] [2024-12-26 01:14:05,737] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-12-26 01:14:07,225] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-12-26 01:14:08,983] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-12-26 01:14:12,085] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-12-26 01:14:15,931] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2024-12-26 01:14:23,531] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-12-26 01:14:33,202] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-26 01:14:34,443] [pool-1-thread-3] Initializing /data/stephane/002007000.flex: [testng] [2024-12-26 01:14:38,886] [pool-1-thread-1] Initializing /data/tamjid/006005000.flex: [testng] [2024-12-26 01:14:43,522] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-26 01:14:53,320] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-12-26 01:15:03,761] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-12-26 01:15:05,145] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-12-26 01:15:06,573] [pool-1-thread-2] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-12-26 01:15:23,221] [pool-1-thread-7] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-26 01:15:24,804] [pool-1-thread-3] Initializing /data/manuel/003003001.flex: [testng] [2024-12-26 01:15:30,166] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-12-26 01:15:54,222] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-26 01:16:01,863] [pool-1-thread-4] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-26 01:16:08,468] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] [2024-12-26 01:16:10,710] [pool-1-thread-3] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-26 01:16:23,304] [pool-1-thread-6] Initializing /data/qa-17190/002002011.flex: [testng] [2024-12-26 01:16:28,929] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-26 01:16:37,294] [pool-1-thread-3] Initializing /data/anatole/001004000.flex: [testng] [2024-12-26 01:16:49,594] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-12-26 01:16:51,977] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 26 minutes 20 seconds Finished: SUCCESS