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Started by upstream project "BIOFORMATS-test-repo" build number 365 originally caused by: Started by upstream project "Trigger" build number 391 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/jenkins4293616700196302586.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_58185_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] 00:50:38,643 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:50:38,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:50:38,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:38,645 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:50:38,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:50:38,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:50:38,646 |-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] 00:50:38,646 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:38,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:50:38,647 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:50:38,647 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:50:38,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:50:38,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:50:38,802 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:50:38,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:50:38,825 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:50:38,830 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:50:38,831 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:50:38,831 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:50:38,831 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:50:38,831 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:50:38,832 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:50:38,832 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 185 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-05 00:50:38,840] [main] java.version = 17.0.2 [testng] 00:50:38,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:50:38,843 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:38,882 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-05_00-50-38.log] [testng] 00:50:38,883 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-05 00:50:38,885] [main] testng.directory = /data [testng] [2025-03-05 00:50:38,885] [main] testng.configDirectory = /config [testng] [2025-03-05 00:50:38,893] [main] testng.multiplier = 1.0 [testng] [2025-03-05 00:50:38,894] [main] testng.in-memory = false [testng] [2025-03-05 00:50:38,894] [main] testng.allow-missing = false [testng] [2025-03-05 00:50:38,894] [main] user.language = en [testng] [2025-03-05 00:50:38,894] [main] user.country = ${user.country} [testng] [2025-03-05 00:50:38,894] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-05 00:51:29,608] [main] ---------------------------------------- [testng] [2025-03-05 00:51:29,608] [main] Total files: 791 [testng] [2025-03-05 00:51:29,608] [main] Scan time: 50.714 s (64 ms/file) [testng] [2025-03-05 00:51:29,608] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-05 00:57:44,297] [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] 00:57:44,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:57:44,298 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:44,299 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-05_00-57-44.log] [testng] 00:57:44,299 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1512d1ec - End of configuration. [testng] [2025-03-05 00:57:45,420] [pool-1-thread-12] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 00:57:45,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:57:45,421 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:45,421 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-05_00-57-45.log] [testng] 00:57:45,422 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44c13bf7 - End of configuration. [testng] [2025-03-05 00:57:51,542] [pool-1-thread-11] Initializing /data/qa-18096/002002001.flex: [testng] 00:57:51,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:57:51,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:51,543 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-05_00-57-51.log] [testng] 00:57:51,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@51a15d4a - End of configuration. [testng] [2025-03-05 00:57:52,313] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:57:52,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:57:52,313 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:52,314 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-05_00-57-52.log] [testng] 00:57:52,314 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b870946 - End of configuration. [testng] [2025-03-05 00:57:59,124] [pool-1-thread-9] Initializing /data/manuel/003003001.flex: [testng] 00:57:59,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:57:59,124 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:57:59,125 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-05_00-57-59.log] [testng] 00:57:59,126 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6bc152a7 - End of configuration. [testng] [2025-03-05 00:58:00,110] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] 00:58:00,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:58:00,111 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:00,111 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-05_00-58-00.log] [testng] 00:58:00,112 |-INFO in ch.qos.logback.core.sift.SiftProcessor@16555ee4 - End of configuration. [testng] [2025-03-05 00:58:02,081] [pool-1-thread-7] Initializing /data/tamjid/006003000.flex: [testng] 00:58:02,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:58:02,081 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:02,082 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-05_00-58-02.log] [testng] 00:58:02,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3c14e80 - End of configuration. [testng] [2025-03-05 00:58:02,990] [pool-1-thread-6] Initializing /data/qa-7469/002002.flex: [testng] 00:58:02,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:58:02,990 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:02,991 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-05_00-58-02.log] [testng] 00:58:02,991 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6db48209 - End of configuration. [testng] [2025-03-05 00:58:03,883] [pool-1-thread-5] Initializing /data/tony/001001000_objects.flex: [testng] 00:58:03,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:58:03,883 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:03,884 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-05_00-58-03.log] [testng] 00:58:03,884 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37bebaee - End of configuration. [testng] [2025-03-05 00:58:04,926] [pool-1-thread-4] Initializing /data/stephane/006013000.flex: [testng] 00:58:04,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:58:04,926 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:04,927 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-05_00-58-04.log] [testng] 00:58:04,927 |-INFO in ch.qos.logback.core.sift.SiftProcessor@fedb565 - End of configuration. [testng] [2025-03-05 00:58:05,875] [pool-1-thread-3] Initializing /data/qa-17190/002002011.flex: [testng] 00:58:05,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:58:05,875 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:05,876 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-05_00-58-05.log] [testng] 00:58:05,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77ad8440 - End of configuration. [testng] [2025-03-05 00:58:06,800] [pool-1-thread-2] Initializing /data/achim/003003000.flex: [testng] 00:58:06,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:58:06,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:58:06,801 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-05_00-58-06.log] [testng] 00:58:06,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@607f1474 - End of configuration. [testng] [2025-03-05 00:58:20,069] [pool-1-thread-8] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-03-05 00:58:21,755] [pool-1-thread-3] Initializing /data/tony/003003000.tiff: [testng] [2025-03-05 00:58:23,522] [pool-1-thread-6] Initializing /data/tony/015002000.tiff: [testng] [2025-03-05 00:58:25,165] [pool-1-thread-5] Initializing /data/tamjid/006005000.flex: [testng] [2025-03-05 00:58:25,911] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-03-05 00:58:31,779] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-03-05 00:58:38,917] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-03-05 00:58:47,032] [pool-1-thread-2] Initializing /data/qa-2983/004007000.flex: [testng] [2025-03-05 00:58:52,083] [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] [2025-03-05 00:58:53,171] [pool-1-thread-5] Initializing /data/tony/test1.flex: [testng] [2025-03-05 00:58:54,366] [pool-1-thread-3] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2025-03-05 00:58:55,585] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2025-03-05 00:58:57,618] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] [2025-03-05 00:59:05,953] [pool-1-thread-2] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2025-03-05 00:59:10,556] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-03-05 00:59:17,939] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] [2025-03-05 00:59:19,338] [pool-1-thread-6] Initializing /data/anatole/001004000.flex: [testng] [2025-03-05 00:59:20,785] [pool-1-thread-5] Initializing /data/stephane/002007000.flex: [testng] [2025-03-05 00:59:22,033] [pool-1-thread-3] Initializing /data/tony/003008000.flex: [testng] [2025-03-05 00:59:23,053] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] [2025-03-05 00:59:29,809] [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] [2025-03-05 00:59:40,068] [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] [2025-03-05 00:59:45,249] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-03-05 00:59:46,657] [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] [2025-03-05 00:59:49,652] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2025-03-05 01:00:01,783] [pool-1-thread-9] Initializing /data/ghislain/test.flex: [testng] [2025-03-05 01:00:09,978] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2025-03-05 01:00:12,939] [pool-1-thread-3] Initializing /data/tamjid/006004000.flex: [testng] [2025-03-05 01:00:22,384] [pool-1-thread-6] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2025-03-05 01:00:31,228] [pool-1-thread-9] 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: 17 minutes 55 seconds Finished: SUCCESS