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Started by upstream project "BIOFORMATS-test-repo" build number 380 originally caused by: Started by upstream project "Trigger" build number 402 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3 [BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins4764103551118021864.sh + '[' flex = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_60119_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] 02:29:10,804 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 02:29:10,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 02:29:10,805 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:29:10,806 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:29:10,806 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:29:10,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:29:10,807 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 02:29:10,807 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:29:10,807 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:29:10,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:29:10,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:29:10,808 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:29:10,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:29:10,970 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:29:10,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:29:10,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:29:10,999 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:29:11,000 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:29:11,000 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:29:11,000 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:29:11,000 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 02:29:11,001 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 02:29:11,001 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 194 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-16 02:29:11,010] [main] java.version = 17.0.2 [testng] 02:29:11,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:29:11,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:29:11,056 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-16_02-29-11.log] [testng] 02:29:11,058 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-16 02:29:11,060] [main] testng.directory = /data [testng] [2025-03-16 02:29:11,060] [main] testng.configDirectory = /config [testng] [2025-03-16 02:29:11,069] [main] testng.multiplier = 1.0 [testng] [2025-03-16 02:29:11,070] [main] testng.in-memory = false [testng] [2025-03-16 02:29:11,070] [main] testng.allow-missing = false [testng] [2025-03-16 02:29:11,070] [main] user.language = en [testng] [2025-03-16 02:29:11,071] [main] user.country = ${user.country} [testng] [2025-03-16 02:29:11,071] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-16 02:35:08,072] [main] ---------------------------------------- [testng] [2025-03-16 02:35:08,072] [main] Total files: 791 [testng] [2025-03-16 02:35:08,072] [main] Scan time: 357.001 s (451 ms/file) [testng] [2025-03-16 02:35:08,072] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-16 02:49:53,938] [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] 02:49:53,938 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:49:53,939 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:49:53,940 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-16_02-49-53.log] [testng] 02:49:53,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6dfe1da5 - End of configuration. [testng] [2025-03-16 02:50:12,645] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 02:50:12,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:50:12,645 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:50:12,646 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-16_02-50-12.log] [testng] 02:50:12,646 |-INFO in ch.qos.logback.core.sift.SiftProcessor@50a1e1d5 - End of configuration. [testng] [2025-03-16 02:51:44,569] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex: [testng] 02:51:44,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:51:44,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:51:44,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-16_02-51-44.log] [testng] 02:51:44,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44c13bf7 - End of configuration. [testng] [2025-03-16 02:52:00,278] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 02:52:00,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:52:00,278 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:52:00,279 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-16_02-52-00.log] [testng] 02:52:00,279 |-INFO in ch.qos.logback.core.sift.SiftProcessor@33e1eeba - End of configuration. [testng] [2025-03-16 02:54:01,495] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] 02:54:01,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:54:01,496 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:01,496 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-16_02-54-01.log] [testng] 02:54:01,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@8660002 - End of configuration. [testng] [2025-03-16 02:54:13,753] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] 02:54:13,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:54:13,753 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:13,754 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-16_02-54-13.log] [testng] 02:54:13,754 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f397a48 - End of configuration. [testng] [2025-03-16 02:54:32,046] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] 02:54:32,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:54:32,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:32,047 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-16_02-54-32.log] [testng] 02:54:32,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52670bb6 - End of configuration. [testng] [2025-03-16 02:54:37,038] [pool-1-thread-6] Initializing /data/qa-7469/002002.flex: [testng] 02:54:37,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:54:37,038 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:37,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-16_02-54-37.log] [testng] 02:54:37,039 |-INFO in ch.qos.logback.core.sift.SiftProcessor@41a79943 - End of configuration. [testng] [2025-03-16 02:54:42,247] [pool-1-thread-5] Initializing /data/tony/001001000_objects.flex: [testng] 02:54:42,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:54:42,247 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:42,248 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-16_02-54-42.log] [testng] 02:54:42,248 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ca95a5 - End of configuration. [testng] [2025-03-16 02:54:48,674] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] 02:54:48,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:54:48,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:48,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-16_02-54-48.log] [testng] 02:54:48,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14f298a6 - End of configuration. [testng] [2025-03-16 02:54:54,166] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] 02:54:54,166 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:54:54,167 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:54,167 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-16_02-54-54.log] [testng] 02:54:54,168 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29bf3889 - End of configuration. [testng] [2025-03-16 02:54:59,841] [pool-1-thread-2] Initializing /data/achim/003003000.flex: [testng] 02:54:59,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:54:59,842 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:54:59,843 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-16_02-54-59.log] [testng] 02:54:59,843 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5cefe1dc - End of configuration. [testng] [2025-03-16 02:55:56,511] [pool-1-thread-8] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-03-16 02:56:04,756] [pool-1-thread-7] Initializing /data/tony/015002000.tiff: [testng] [2025-03-16 02:56:13,338] [pool-1-thread-6] Initializing /data/tamjid/006005000.flex: [testng] [2025-03-16 02:56:18,326] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-03-16 02:56:46,636] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] [2025-03-16 02:56:55,209] [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] [2025-03-16 02:57:02,537] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-03-16 02:58:14,564] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2025-03-16 02:58:33,795] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-03-16 02:58:41,572] [pool-1-thread-6] Initializing /data/tony/test1.flex: [testng] [2025-03-16 02:58:45,511] [pool-1-thread-9] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-03-16 02:58:48,713] [pool-1-thread-7] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-03-16 02:58:56,963] [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] [2025-03-16 02:59:13,825] [pool-1-thread-2] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-03-16 02:59:45,051] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-03-16 03:00:22,714] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-03-16 03:00:30,956] [pool-1-thread-8] Initializing /data/anatole/001004000.flex: [testng] [2025-03-16 03:00:42,906] [pool-1-thread-9] Initializing /data/stephane/002007000.flex: [testng] [2025-03-16 03:00:57,155] [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] [2025-03-16 03:01:03,150] [pool-1-thread-1] Initializing /data/tony/003008000.flex: [testng] [2025-03-16 03:01:27,799] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-03-16 03:02:04,136] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-03-16 03:02:34,669] [pool-1-thread-5] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-03-16 03:02:40,813] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2025-03-16 03:02:48,213] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-03-16 03:03:39,436] [pool-1-thread-3] Initializing /data/ghislain/test.flex: [testng] [2025-03-16 03:04:21,016] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-03-16 03:04:33,866] [pool-1-thread-9] Initializing /data/tamjid/006004000.flex: [testng] [2025-03-16 03:04:55,775] [pool-1-thread-6] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-03-16 03:05:40,869] [pool-1-thread-3] Initializing /data/qa-18096/002003001.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 74 minutes 39 seconds Finished: SUCCESS