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Started by upstream project "BIOFORMATS-test-repo" build number 239 originally caused by: Started by upstream project "Trigger" build number 264 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/jenkins2283637056931216188.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_37569_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] 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] 00:55:26,314 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:55:26,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:55:26,315 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:26,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:26,316 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:55:26,317 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:55:26,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:55:26,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:26,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:26,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:55:26,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:55:26,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:55:26,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:55:26,479 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:55:26,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:55:26,502 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:55:26,507 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:55:26,507 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:55:26,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:55:26,508 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:55:26,508 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:55:26,509 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:55:26,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-30 00:55:26,518] [main] java.version = 17.0.2 [testng] 00:55:26,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:55:26,521 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:26,562 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-30_00-55-26.log] [testng] 00:55:26,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-10-30 00:55:26,565] [main] testng.directory = /data [testng] [2024-10-30 00:55:26,566] [main] testng.configDirectory = /config [testng] [2024-10-30 00:55:26,574] [main] testng.multiplier = 1.0 [testng] [2024-10-30 00:55:26,575] [main] testng.in-memory = false [testng] [2024-10-30 00:55:26,575] [main] testng.allow-missing = false [testng] [2024-10-30 00:55:26,575] [main] user.language = en [testng] [2024-10-30 00:55:26,575] [main] user.country = ${user.country} [testng] [2024-10-30 00:55:26,575] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-30 01:05:06,244] [main] ---------------------------------------- [testng] [2024-10-30 01:05:06,244] [main] Total files: 791 [testng] [2024-10-30 01:05:06,245] [main] Scan time: 579.668 s (732 ms/file) [testng] [2024-10-30 01:05:06,245] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-30 01:10:13,127] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] 01:10:13,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:10:13,127 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:13,128 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-30_01-10-13.log] [testng] 01:10:13,129 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4b212fbe - End of configuration. [testng] [2024-10-30 01:10:13,554] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 01:10:13,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:10:13,554 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:13,555 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-30_01-10-13.log] [testng] 01:10:13,555 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1d06df06 - End of configuration. [testng] [2024-10-30 01:10:14,002] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] 01:10:14,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:10:14,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:14,002 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-30_01-10-14.log] [testng] 01:10:14,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44c13bf7 - End of configuration. [testng] [2024-10-30 01:10:14,437] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:10:14,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:10:14,437 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:14,438 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-30_01-10-14.log] [testng] 01:10:14,438 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f094931 - End of configuration. [testng] [2024-10-30 01:10:15,318] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] 01:10:15,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:10:15,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:15,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-30_01-10-15.log] [testng] 01:10:15,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6da861eb - End of configuration. [testng] [2024-10-30 01:10:15,755] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex: [testng] 01:10:15,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:10:15,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:15,756 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-30_01-10-15.log] [testng] 01:10:15,756 |-INFO in ch.qos.logback.core.sift.SiftProcessor@521e5250 - End of configuration. [testng] [2024-10-30 01:10:16,229] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 01:10:16,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:10:16,229 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:16,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-30_01-10-16.log] [testng] 01:10:16,230 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6db48209 - End of configuration. [testng] [2024-10-30 01:10:19,641] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:10:19,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:10:19,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:19,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-30_01-10-19.log] [testng] 01:10:19,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ad8440 - End of configuration. [testng] [2024-10-30 01:10:23,529] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] 01:10:23,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:10:23,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:23,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-30_01-10-23.log] [testng] 01:10:23,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@607f1474 - End of configuration. [testng] [2024-10-30 01:10:24,009] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] 01:10:24,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:10:24,010 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:24,010 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-30_01-10-24.log] [testng] 01:10:24,010 |-INFO in ch.qos.logback.core.sift.SiftProcessor@18e890e2 - End of configuration. [testng] [2024-10-30 01:10:25,081] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:10:25,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:10:25,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:25,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-30_01-10-25.log] [testng] 01:10:25,082 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e21092d - End of configuration. [testng] [2024-10-30 01:10:29,334] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] 01:10:29,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:10:29,335 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:10:29,336 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-30_01-10-29.log] [testng] 01:10:29,336 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4944ac4d - End of configuration. [testng] [2024-10-30 01:10:37,244] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-10-30 01:10:42,277] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2024-10-30 01:10:42,940] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-30 01:10:43,527] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-30 01:10:44,214] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-10-30 01:10:48,112] [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] [2024-10-30 01:10:48,780] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-30 01:10:49,427] [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] [2024-10-30 01:10:53,100] [pool-1-thread-5] Initializing /data/tony/test.tiff: [testng] [2024-10-30 01:10:54,303] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-30 01:10:59,047] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] [2024-10-30 01:10:59,756] [pool-1-thread-1] Initializing /data/achim/003003000.flex: [testng] [2024-10-30 01:11:03,500] [pool-1-thread-12] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-30 01:11:04,145] [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] [2024-10-30 01:11:06,476] [pool-1-thread-9] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-30 01:11:07,124] [pool-1-thread-11] Initializing /data/anatole/001004000.flex: [testng] [2024-10-30 01:11:08,034] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2024-10-30 01:11:09,763] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-30 01:11:18,956] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2024-10-30 01:11:21,616] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] [2024-10-30 01:11:23,651] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-10-30 01:11:25,291] [pool-1-thread-5] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-30 01:11:27,122] [pool-1-thread-4] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-30 01:11:34,288] [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] [2024-10-30 01:11:40,558] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2024-10-30 01:11:44,823] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-10-30 01:11:48,817] [pool-1-thread-11] Initializing /data/qa-17190/002002011.flex: [testng] [2024-10-30 01:11:51,749] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-30 01:11:58,995] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-30 01:12:10,159] [pool-1-thread-12] Initializing /data/tony/test1.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 21 minutes 57 seconds Finished: SUCCESS