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Started by upstream project "BIOFORMATS-test-repo" build number 1 originally caused by: Started by upstream project "Trigger" build number 1 originally caused by: Started by user devspace Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins10948119322211861113.sh + '[' flex = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_59_merge_ci -v /uod/idr/repos/curated/flex:/data -v /uod/idr-scratch/devspace/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 16:12:27,116 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 16:12:27,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 16:12:27,117 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:12:27,118 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 16:12:27,118 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 16:12:27,119 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 16:12:27,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 16:12:27,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:12:27,119 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 16:12:27,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 16:12:27,120 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 16:12:27,121 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 16:12:27,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 16:12:27,290 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 16:12:27,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 16:12:27,321 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 16:12:27,328 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 16:12:27,328 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 16:12:27,328 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 16:12:27,328 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 16:12:27,328 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 16:12:27,329 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 16:12:27,329 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 210 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-03-14 16:12:27,339] [main] java.version = 21 [testng] 16:12:27,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:12:27,343 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:12:27,386 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-03-14_16-12-27.log] [testng] 16:12:27,387 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-03-14 16:12:27,389] [main] testng.directory = /data [testng] [2024-03-14 16:12:27,389] [main] testng.configDirectory = /config [testng] [2024-03-14 16:12:27,398] [main] testng.multiplier = 1.0 [testng] [2024-03-14 16:12:27,399] [main] testng.in-memory = false [testng] [2024-03-14 16:12:27,399] [main] testng.allow-missing = false [testng] [2024-03-14 16:12:27,399] [main] user.language = en [testng] [2024-03-14 16:12:27,399] [main] user.country = ${user.country} [testng] [2024-03-14 16:12:27,399] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-03-14 16:12:44,599] [main] ---------------------------------------- [testng] [2024-03-14 16:12:44,599] [main] Total files: 791 [testng] [2024-03-14 16:12:44,599] [main] Scan time: 17.2 s (21 ms/file) [testng] [2024-03-14 16:12:44,600] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-03-14 16:18:32,742] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 16:18:32,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 16:18:32,742 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:32,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-03-14_16-18-32.log] [testng] 16:18:32,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54192236 - End of configuration. [testng] [2024-03-14 16:18:33,130] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] 16:18:33,130 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 16:18:33,131 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:33,131 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-03-14_16-18-33.log] [testng] 16:18:33,132 |-INFO in ch.qos.logback.core.sift.SiftProcessor@520bea7c - End of configuration. [testng] [2024-03-14 16:18:33,339] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 16:18:33,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 16:18:33,339 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:33,341 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-03-14_16-18-33.log] [testng] 16:18:33,341 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7055fa48 - End of configuration. [testng] [2024-03-14 16:18:33,551] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 16:18:33,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 16:18:33,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:33,552 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-03-14_16-18-33.log] [testng] 16:18:33,552 |-INFO in ch.qos.logback.core.sift.SiftProcessor@176b6f5e - End of configuration. [testng] [2024-03-14 16:18:33,779] [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] 16:18:33,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 16:18:33,779 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:33,780 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-03-14_16-18-33.log] [testng] 16:18:33,781 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b96de96 - End of configuration. [testng] [2024-03-14 16:18:34,022] [pool-1-thread-8] Initializing /data/tony/test1.flex: [testng] 16:18:34,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 16:18:34,022 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:34,023 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-03-14_16-18-34.log] [testng] 16:18:34,024 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36b1fce1 - End of configuration. [testng] [2024-03-14 16:18:34,285] [pool-1-thread-7] Initializing /data/tony/001014000 - from flex.tif: [testng] 16:18:34,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 16:18:34,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:34,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-03-14_16-18-34.log] [testng] 16:18:34,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@742da30 - End of configuration. [testng] [2024-03-14 16:18:34,720] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex: [testng] 16:18:34,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 16:18:34,720 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:34,721 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-03-14_16-18-34.log] [testng] 16:18:34,721 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2a5a2ede - End of configuration. [testng] [2024-03-14 16:18:34,941] [pool-1-thread-5] Initializing /data/stephane/006013000.flex: [testng] 16:18:34,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 16:18:34,941 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:34,942 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-03-14_16-18-34.log] [testng] 16:18:34,942 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4137d3bd - End of configuration. [testng] [2024-03-14 16:18:35,198] [pool-1-thread-4] Initializing /data/achim/003003000.flex: [testng] 16:18:35,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 16:18:35,198 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:35,199 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-03-14_16-18-35.log] [testng] 16:18:35,199 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f035dac - End of configuration. [testng] [2024-03-14 16:18:35,560] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] 16:18:35,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 16:18:35,560 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:35,561 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-03-14_16-18-35.log] [testng] 16:18:35,562 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ca71327 - End of configuration. [testng] [2024-03-14 16:18:35,788] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] 16:18:35,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 16:18:35,788 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:18:35,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-03-14_16-18-35.log] [testng] 16:18:35,789 |-INFO in ch.qos.logback.core.sift.SiftProcessor@326191 - End of configuration. [testng] [2024-03-14 16:18:39,812] [pool-1-thread-8] Initializing /data/tony/003003000.tiff: [testng] [2024-03-14 16:18:40,357] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] [2024-03-14 16:18:40,563] [pool-1-thread-1] Initializing /data/tamjid/006004000.flex: [testng] [2024-03-14 16:18:40,751] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2024-03-14 16:18:40,967] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-03-14 16:18:42,871] [pool-1-thread-3] Initializing /data/manuel/003003001.flex: [testng] [2024-03-14 16:18:43,103] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-03-14 16:18:45,270] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2024-03-14 16:18:45,659] [pool-1-thread-9] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-03-14 16:18:46,158] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-03-14 16:18:48,607] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-03-14 16:18:51,135] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-03-14 16:18:51,666] [pool-1-thread-5] Initializing /data/qa-18096/002003001.flex: [testng] [2024-03-14 16:18:52,023] [pool-1-thread-6] Initializing /data/qa-17190/002002011.flex: [testng] [2024-03-14 16:18:54,760] [pool-1-thread-12] Initializing /data/qa-7469/002002.flex: [testng] [2024-03-14 16:18:55,527] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-03-14 16:18:57,235] [pool-1-thread-6] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-03-14 16:18:58,078] [pool-1-thread-4] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-03-14 16:18:58,474] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-03-14 16:19:02,364] [pool-1-thread-5] Initializing /data/anatole/001004000.flex: [testng] [2024-03-14 16:19:02,865] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-03-14 16:19:03,368] [pool-1-thread-2] Initializing /data/tony/015002000.tiff: [testng] [2024-03-14 16:19:06,497] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-03-14 16:19:12,282] [pool-1-thread-10] Initializing /data/tony/003008000.flex: [testng] [2024-03-14 16:19:12,921] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-03-14 16:19:16,872] [pool-1-thread-4] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-03-14 16:19:22,502] [pool-1-thread-3] Initializing /data/qa-18096/002002001.flex: [testng] [2024-03-14 16:19:26,613] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2024-03-14 16:19:27,997] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-03-14 16:19:31,706] [pool-1-thread-10] Initializing /data/tony/test.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 11 minutes 48 seconds Finished: SUCCESS