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Started by upstream project "BIOFORMATS-test-repo" build number 288 originally caused by: Started by upstream project "Trigger" build number 307 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/jenkins3809074355227012013.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45478_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:49:24,099 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:49:24,100 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 01:49:24,100 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:49:24,101 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:49:24,101 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:49:24,102 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:49:24,102 |-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] 01:49:24,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:49:24,102 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:49:24,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:49:24,103 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:49:24,104 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:49:24,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:49:24,294 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:49:24,318 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:49:24,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:49:24,325 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:49:24,325 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:49:24,325 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:49:24,326 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:49:24,326 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 01:49:24,326 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 01:49:24,326 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 224 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-12 01:49:24,336] [main] java.version = 21 [testng] 01:49:24,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:49:24,340 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:24,383 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-12_01-49-24.log] [testng] 01:49:24,385 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-12 01:49:24,386] [main] testng.directory = /data [testng] [2024-12-12 01:49:24,386] [main] testng.configDirectory = /config [testng] [2024-12-12 01:49:24,395] [main] testng.multiplier = 1.0 [testng] [2024-12-12 01:49:24,395] [main] testng.in-memory = false [testng] [2024-12-12 01:49:24,396] [main] testng.allow-missing = false [testng] [2024-12-12 01:49:24,396] [main] user.language = en [testng] [2024-12-12 01:49:24,396] [main] user.country = ${user.country} [testng] [2024-12-12 01:49:24,396] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-12 01:54:35,626] [main] ---------------------------------------- [testng] [2024-12-12 01:54:35,626] [main] Total files: 791 [testng] [2024-12-12 01:54:35,626] [main] Scan time: 311.23 s (393 ms/file) [testng] [2024-12-12 01:54:35,626] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-12 02:04:42,815] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 02:04:42,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:04:42,816 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:42,817 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-12_02-04-42.log] [testng] 02:04:42,818 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9618e9e - End of configuration. [testng] [2024-12-12 02:04:55,759] [pool-1-thread-12] Initializing /data/manuel/003003001.flex: [testng] 02:04:55,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:04:55,760 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:55,760 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-12_02-04-55.log] [testng] 02:04:55,761 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c2a1d3c - End of configuration. [testng] [2024-12-12 02:04:59,046] [pool-1-thread-11] Initializing /data/stephane/002007000.flex: [testng] 02:04:59,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:04:59,047 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:04:59,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-12_02-04-59.log] [testng] 02:04:59,048 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6730cdf6 - End of configuration. [testng] [2024-12-12 02:05:02,652] [pool-1-thread-10] Initializing /data/qa-17190/002002011.flex: [testng] 02:05:02,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:05:02,652 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:02,653 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-12_02-05-02.log] [testng] 02:05:02,653 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9c8979c - End of configuration. [testng] [2024-12-12 02:05:06,953] [pool-1-thread-9] Initializing /data/tony/015002000.tiff: [testng] 02:05:06,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:05:06,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:06,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-12_02-05-06.log] [testng] 02:05:06,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32b1b325 - End of configuration. [testng] [2024-12-12 02:05:11,730] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] 02:05:11,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:05:11,730 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:11,731 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-12_02-05-11.log] [testng] 02:05:11,731 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7da0858c - End of configuration. [testng] [2024-12-12 02:05:23,774] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 02:05:23,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:05:23,775 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:23,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-12_02-05-23.log] [testng] 02:05:23,776 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78792ff0 - End of configuration. [testng] [2024-12-12 02:05:25,552] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 02:05:25,552 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:05:25,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:25,554 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-12_02-05-25.log] [testng] 02:05:25,554 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5da9470e - End of configuration. [testng] [2024-12-12 02:05:37,995] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] 02:05:37,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:05:37,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:37,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-12_02-05-37.log] [testng] 02:05:37,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c47ab5 - End of configuration. [testng] [2024-12-12 02:05:39,676] [pool-1-thread-4] Initializing /data/tony/003008000.flex: [testng] 02:05:39,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:05:39,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:39,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-12_02-05-39.log] [testng] 02:05:39,677 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6fdb0be0 - End of configuration. [testng] [2024-12-12 02:05:41,404] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 02:05:41,404 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:05:41,405 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:41,405 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-12_02-05-41.log] [testng] 02:05:41,405 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6789bdc5 - End of configuration. [testng] [2024-12-12 02:05:43,271] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] 02:05:43,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:05:43,271 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:05:43,271 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-12_02-05-43.log] [testng] 02:05:43,272 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78e15646 - End of configuration. [testng] [2024-12-12 02:06:06,541] [pool-1-thread-9] Initializing /data/tony/test.tiff: [testng] [2024-12-12 02:06:10,421] [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] [2024-12-12 02:06:12,251] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-12-12 02:06:13,970] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-12-12 02:06:27,327] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-12 02:06:32,795] [pool-1-thread-4] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-12 02:06:41,379] [pool-1-thread-3] Initializing /data/achim/003003000.flex: [testng] [2024-12-12 02:06:43,497] [pool-1-thread-7] Initializing /data/stephane/006013000.flex: [testng] [2024-12-12 02:06:52,380] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-12-12 02:07:10,666] [pool-1-thread-12] Initializing /data/anatole/001004000.flex: [testng] [2024-12-12 02:07:16,953] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-12 02:07:24,523] [pool-1-thread-10] Initializing /data/tamjid/006004000.flex: [testng] [2024-12-12 02:07:26,620] [pool-1-thread-5] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-12-12 02:07:42,761] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-12-12 02:08:08,135] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-12 02:08:10,657] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-12-12 02:08:32,933] [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] [2024-12-12 02:08:35,591] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-12 02:08:49,916] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-12-12 02:09:10,883] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-12 02:09:36,983] [pool-1-thread-7] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-12 02:09:39,525] [pool-1-thread-12] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-12 02:09:42,655] [pool-1-thread-2] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-12 02:10:08,267] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] [2024-12-12 02:10:13,345] [pool-1-thread-7] Initializing /data/tony/003003000.tiff: [testng] [2024-12-12 02:10:21,240] [pool-1-thread-12] Initializing /data/qa-2983/004007000.flex: [testng] [2024-12-12 02:10:23,747] [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] [2024-12-12 02:10:26,448] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] [2024-12-12 02:10:50,167] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-12 02:10:53,047] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 39 minutes 46 seconds Finished: SUCCESS