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Started by upstream project "BIOFORMATS-test-repo" build number 275 originally caused by: Started by upstream project "Trigger" build number 296 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins4493271561191412563.sh + '[' flex = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_43344_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] 00:47:56,492 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:47:56,493 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:47:56,493 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:47:56,494 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:47:56,495 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:47:56,495 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:47:56,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:47:56,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:47:56,496 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:47:56,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:47:56,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:47:56,497 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:47:56,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:47:56,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:47:56,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:47:56,691 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:47:56,697 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:47:56,697 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:47:56,697 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:47:56,698 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:47:56,698 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:47:56,699 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:47:56,699 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 203 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-01 00:47:56,708] [main] java.version = 17.0.2 [testng] 00:47:56,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:47:56,711 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:56,752 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-01_00-47-56.log] [testng] 00:47:56,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-12-01 00:47:56,756] [main] testng.directory = /data [testng] [2024-12-01 00:47:56,756] [main] testng.configDirectory = /config [testng] [2024-12-01 00:47:56,765] [main] testng.multiplier = 1.0 [testng] [2024-12-01 00:47:56,766] [main] testng.in-memory = false [testng] [2024-12-01 00:47:56,766] [main] testng.allow-missing = false [testng] [2024-12-01 00:47:56,766] [main] user.language = en [testng] [2024-12-01 00:47:56,766] [main] user.country = ${user.country} [testng] [2024-12-01 00:47:56,766] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-01 00:48:27,178] [main] ---------------------------------------- [testng] [2024-12-01 00:48:27,178] [main] Total files: 791 [testng] [2024-12-01 00:48:27,178] [main] Scan time: 30.412 s (38 ms/file) [testng] [2024-12-01 00:48:27,179] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-01 00:52:44,043] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] 00:52:44,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:52:44,044 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:44,045 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-01_00-52-44.log] [testng] 00:52:44,046 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60eb9ea - End of configuration. [testng] [2024-12-01 00:52:44,509] [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] 00:52:44,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:52:44,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:44,510 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-01_00-52-44.log] [testng] 00:52:44,510 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3d416c16 - End of configuration. [testng] [2024-12-01 00:52:44,952] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] 00:52:44,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:52:44,953 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:44,954 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-01_00-52-44.log] [testng] 00:52:44,954 |-INFO in ch.qos.logback.core.sift.SiftProcessor@750ddb90 - End of configuration. [testng] [2024-12-01 00:52:45,416] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] 00:52:45,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:52:45,416 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:45,417 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-01_00-52-45.log] [testng] 00:52:45,417 |-INFO in ch.qos.logback.core.sift.SiftProcessor@509508d6 - End of configuration. [testng] [2024-12-01 00:52:46,360] [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] 00:52:46,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:52:46,360 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:46,361 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-01_00-52-46.log] [testng] 00:52:46,361 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4013e035 - End of configuration. [testng] [2024-12-01 00:52:46,873] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex: [testng] 00:52:46,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:52:46,873 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:46,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-01_00-52-46.log] [testng] 00:52:46,874 |-INFO in ch.qos.logback.core.sift.SiftProcessor@780a43ec - End of configuration. [testng] [2024-12-01 00:52:47,369] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 00:52:47,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:52:47,369 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:47,370 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-01_00-52-47.log] [testng] 00:52:47,370 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cf62e71 - End of configuration. [testng] [2024-12-01 00:52:51,251] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:52:51,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:52:51,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:51,251 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-01_00-52-51.log] [testng] 00:52:51,252 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7f06a2b2 - End of configuration. [testng] [2024-12-01 00:52:55,895] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] 00:52:55,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:52:55,895 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:55,896 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-01_00-52-55.log] [testng] 00:52:55,896 |-INFO in ch.qos.logback.core.sift.SiftProcessor@741703f5 - End of configuration. [testng] [2024-12-01 00:52:56,511] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] 00:52:56,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:52:56,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:56,511 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-01_00-52-56.log] [testng] 00:52:56,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6efb14cb - End of configuration. [testng] [2024-12-01 00:52:57,920] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 00:52:57,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:52:57,920 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:57,921 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-01_00-52-57.log] [testng] 00:52:57,921 |-INFO in ch.qos.logback.core.sift.SiftProcessor@563e357e - End of configuration. [testng] [2024-12-01 00:53:03,501] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] 00:53:03,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:53:03,501 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:53:03,502 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-01_00-53-03.log] [testng] 00:53:03,502 |-INFO in ch.qos.logback.core.sift.SiftProcessor@521e5250 - End of configuration. [testng] [2024-12-01 00:53:15,090] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-12-01 00:53:21,818] [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] [2024-12-01 00:53:22,828] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-01 00:53:23,766] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-01 00:53:24,540] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-12-01 00:53:25,512] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-12-01 00:53:26,408] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-01 00:53:27,316] [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] [2024-12-01 00:53:34,401] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] [2024-12-01 00:53:36,087] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-12-01 00:53:42,110] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] [2024-12-01 00:53:43,025] [pool-1-thread-1] Initializing /data/achim/003003000.flex: [testng] [2024-12-01 00:53:43,923] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex: [testng] [2024-12-01 00:53:44,692] [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] [2024-12-01 00:53:49,327] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-01 00:53:50,111] [pool-1-thread-12] Initializing /data/anatole/001004000.flex: [testng] [2024-12-01 00:53:53,265] [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] [2024-12-01 00:53:56,025] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-12-01 00:54:04,919] [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] [2024-12-01 00:54:07,827] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-12-01 00:54:08,715] [pool-1-thread-4] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-01 00:54:10,509] [pool-1-thread-1] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-01 00:54:16,719] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-01 00:54:22,087] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-12-01 00:54:25,733] [pool-1-thread-2] Initializing /data/tony/015002000.tiff: [testng] [2024-12-01 00:54:30,371] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-12-01 00:54:33,254] [pool-1-thread-11] Initializing /data/qa-17190/002002011.flex: [testng] [2024-12-01 00:54:39,397] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-01 00:54:45,985] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-01 00:55:02,258] [pool-1-thread-2] 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: 12 minutes 17 seconds Finished: SUCCESS