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Started by upstream project "BIOFORMATS-test-repo" build number 312 originally caused by: Started by upstream project "Trigger" build number 334 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/jenkins7588314627148037638.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_49435_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] 00:55:09,459 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:55:09,461 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:55:09,461 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:09,462 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:55:09,462 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:55:09,462 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:55:09,463 |-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] 00:55:09,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:09,463 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:55:09,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:55:09,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:55:09,464 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:55:09,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:55:09,625 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:55:09,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:55:09,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:55:09,653 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:55:09,653 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:55:09,654 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:55:09,654 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:55:09,654 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:55:09,655 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:55:09,655 |-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] [2025-01-08 00:55:09,664] [main] java.version = 17.0.2 [testng] 00:55:09,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:55:09,668 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:55:09,724 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-01-08_00-55-09.log] [testng] 00:55:09,727 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2025-01-08 00:55:09,729] [main] testng.directory = /data [testng] [2025-01-08 00:55:09,730] [main] testng.configDirectory = /config [testng] [2025-01-08 00:55:09,743] [main] testng.multiplier = 1.0 [testng] [2025-01-08 00:55:09,745] [main] testng.in-memory = false [testng] [2025-01-08 00:55:09,745] [main] testng.allow-missing = false [testng] [2025-01-08 00:55:09,745] [main] user.language = en [testng] [2025-01-08 00:55:09,745] [main] user.country = ${user.country} [testng] [2025-01-08 00:55:09,745] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-01-08 00:55:57,065] [main] ---------------------------------------- [testng] [2025-01-08 00:55:57,065] [main] Total files: 791 [testng] [2025-01-08 00:55:57,066] [main] Scan time: 47.319 s (59 ms/file) [testng] [2025-01-08 00:55:57,066] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-01-08 01:02:04,786] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 01:02:04,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:02:04,787 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:04,789 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-01-08_01-02-04.log] [testng] 01:02:04,790 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69796b3a - End of configuration. [testng] [2025-01-08 01:02:05,406] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 01:02:05,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:02:05,406 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:05,407 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-01-08_01-02-05.log] [testng] 01:02:05,408 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2aea48b7 - End of configuration. [testng] [2025-01-08 01:02:06,606] [pool-1-thread-11] Initializing /data/ghislain/test.flex: [testng] 01:02:06,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:02:06,606 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:06,607 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-01-08_01-02-06.log] [testng] 01:02:06,608 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4931209 - End of configuration. [testng] [2025-01-08 01:02:07,428] [pool-1-thread-10] Initializing /data/tamjid/006005000.flex: [testng] 01:02:07,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:02:07,428 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:07,429 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-01-08_01-02-07.log] [testng] 01:02:07,429 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2b16d39c - End of configuration. [testng] [2025-01-08 01:02:08,434] [pool-1-thread-9] Initializing /data/tamjid/006003000.flex: [testng] 01:02:08,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:02:08,435 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:08,435 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-01-08_01-02-08.log] [testng] 01:02:08,436 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16f5f455 - End of configuration. [testng] [2025-01-08 01:02:09,093] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] 01:02:09,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:02:09,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:09,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-01-08_01-02-09.log] [testng] 01:02:09,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1c9bd09c - End of configuration. [testng] [2025-01-08 01:02:09,925] [pool-1-thread-7] Initializing /data/qa-2983/004007000.flex: [testng] 01:02:09,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:02:09,925 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:09,926 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-01-08_01-02-09.log] [testng] 01:02:09,926 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3f33869 - End of configuration. [testng] [2025-01-08 01:02:10,703] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] 01:02:10,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:02:10,704 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:10,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-01-08_01-02-10.log] [testng] 01:02:10,705 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75fbbd9f - End of configuration. [testng] [2025-01-08 01:02:16,850] [pool-1-thread-5] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:02:16,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:02:16,851 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:16,851 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-01-08_01-02-16.log] [testng] 01:02:16,852 |-INFO in ch.qos.logback.core.sift.SiftProcessor@176382f5 - End of configuration. [testng] [2025-01-08 01:02:17,621] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:02:17,621 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:02:17,622 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:17,622 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-01-08_01-02-17.log] [testng] 01:02:17,623 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eb0c2da - End of configuration. [testng] [2025-01-08 01:02:24,203] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex: [testng] 01:02:24,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:02:24,203 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:24,204 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-01-08_01-02-24.log] [testng] 01:02:24,204 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78ec7cc2 - End of configuration. [testng] [2025-01-08 01:02:25,397] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:02:25,397 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:02:25,398 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:25,398 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-01-08_01-02-25.log] [testng] 01:02:25,399 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38105904 - End of configuration. [testng] [2025-01-08 01:02:47,314] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-01-08 01:02:48,219] [pool-1-thread-9] Initializing /data/qa-17190/002002011.flex: [testng] [2025-01-08 01:02:49,225] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2025-01-08 01:02:49,999] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-01-08 01:02:56,052] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-01-08 01:03:03,097] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-01-08 01:03:05,590] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-01-08 01:03:15,321] [pool-1-thread-9] Initializing /data/tony/001001000_objects.flex: [testng] [2025-01-08 01:03:16,302] [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] [2025-01-08 01:03:20,843] [pool-1-thread-3] Initializing /data/stephane/006013000.flex: [testng] [2025-01-08 01:03:24,332] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2025-01-08 01:03:30,368] [pool-1-thread-9] Initializing /data/qa-7469/002002.flex: [testng] [2025-01-08 01:03:34,985] [pool-1-thread-10] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-01-08 01:03:36,959] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-01-08 01:03:44,915] [pool-1-thread-12] Initializing /data/tony/015002000.tiff: [testng] [2025-01-08 01:03:46,937] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-01-08 01:03:52,977] [pool-1-thread-3] Initializing /data/manuel/003003001.flex: [testng] [2025-01-08 01:03:54,226] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2025-01-08 01:04:00,647] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2025-01-08 01:04:11,266] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2025-01-08 01:04:13,384] [pool-1-thread-12] Initializing /data/tony/test.tiff: [testng] [2025-01-08 01:04:20,822] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2025-01-08 01:04:22,805] [pool-1-thread-8] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-01-08 01:04:26,592] [pool-1-thread-1] Initializing /data/tony/003003000.tiff: [testng] [2025-01-08 01:04:29,689] [pool-1-thread-12] Initializing /data/achim/003003000.flex: [testng] [2025-01-08 01:04:35,417] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-01-08 01:04:42,360] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-01-08 01:04:44,499] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-01-08 01:04:46,551] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [2025-01-08 01:04:56,121] [pool-1-thread-12] Initializing /data/tony/001014000 - from flex.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 20 minutes 19 seconds Finished: SUCCESS