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Started by upstream project "BIOFORMATS-test-repo" build number 261 originally caused by: Started by upstream project "Trigger" build number 285 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/jenkins2199887561566024432.sh + '[' flex = slidebook ']' ++ date +%u + '[' 3 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_41177_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] 01:00:49,629 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:00:49,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 01:00:49,630 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:00:49,631 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:00:49,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:00:49,632 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:00:49,632 |-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] 01:00:49,632 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:00:49,633 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:00:49,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:00:49,633 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:00:49,634 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:00:49,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:00:49,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:00:49,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:00:49,815 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:00:49,820 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:00:49,821 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:00:49,821 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:00:49,821 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:00:49,821 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 01:00:49,822 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 01:00:49,822 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 189 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-20 01:00:49,831] [main] java.version = 17.0.2 [testng] 01:00:49,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:00:49,834 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:00:49,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-20_01-00-49.log] [testng] 01:00:49,876 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-20 01:00:49,877] [main] testng.directory = /data [testng] [2024-11-20 01:00:49,878] [main] testng.configDirectory = /config [testng] [2024-11-20 01:00:49,886] [main] testng.multiplier = 1.0 [testng] [2024-11-20 01:00:49,887] [main] testng.in-memory = false [testng] [2024-11-20 01:00:49,887] [main] testng.allow-missing = false [testng] [2024-11-20 01:00:49,887] [main] user.language = en [testng] [2024-11-20 01:00:49,887] [main] user.country = ${user.country} [testng] [2024-11-20 01:00:49,887] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-20 01:02:42,578] [main] ---------------------------------------- [testng] [2024-11-20 01:02:42,578] [main] Total files: 791 [testng] [2024-11-20 01:02:42,578] [main] Scan time: 112.691 s (142 ms/file) [testng] [2024-11-20 01:02:42,578] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-20 01:08:49,029] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] 01:08:49,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:08:49,029 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:49,030 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-20_01-08-49.log] [testng] 01:08:49,031 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56bc81db - End of configuration. [testng] [2024-11-20 01:08:49,860] [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] 01:08:49,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:08:49,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:49,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-20_01-08-49.log] [testng] 01:08:49,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44c13bf7 - End of configuration. [testng] [2024-11-20 01:08:50,756] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] 01:08:50,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:08:50,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:50,757 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-20_01-08-50.log] [testng] 01:08:50,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2f094931 - End of configuration. [testng] [2024-11-20 01:08:51,666] [pool-1-thread-10] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:08:51,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:08:51,666 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:51,667 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-20_01-08-51.log] [testng] 01:08:51,667 |-INFO in ch.qos.logback.core.sift.SiftProcessor@9859b7d - End of configuration. [testng] [2024-11-20 01:08:53,535] [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] 01:08:53,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:08:53,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:53,536 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-20_01-08-53.log] [testng] 01:08:53,536 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63879347 - End of configuration. [testng] [2024-11-20 01:08:54,418] [pool-1-thread-8] Initializing /data/tamjid/006004000.flex: [testng] 01:08:54,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:08:54,418 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:54,418 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-20_01-08-54.log] [testng] 01:08:54,419 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3b8b4e37 - End of configuration. [testng] [2024-11-20 01:08:55,349] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 01:08:55,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:08:55,349 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:08:55,350 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-20_01-08-55.log] [testng] 01:08:55,350 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55896030 - End of configuration. [testng] [2024-11-20 01:09:02,164] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:09:02,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:09:02,165 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:09:02,166 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-20_01-09-02.log] [testng] 01:09:02,166 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e21092d - End of configuration. [testng] [2024-11-20 01:09:09,744] [pool-1-thread-5] Initializing /data/qa-2983/004007000.flex: [testng] 01:09:09,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:09:09,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:09:09,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-20_01-09-09.log] [testng] 01:09:09,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4944ac4d - End of configuration. [testng] [2024-11-20 01:09:10,716] [pool-1-thread-4] Initializing /data/tony/003003000.tiff: [testng] 01:09:10,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:09:10,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:09:10,716 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-20_01-09-10.log] [testng] 01:09:10,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@68dfff08 - End of configuration. [testng] [2024-11-20 01:09:12,846] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:09:12,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:09:12,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:09:12,847 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-20_01-09-12.log] [testng] 01:09:12,847 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ef87e45 - End of configuration. [testng] [2024-11-20 01:09:21,213] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] 01:09:21,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:09:21,213 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:09:21,214 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-20_01-09-21.log] [testng] 01:09:21,214 |-INFO in ch.qos.logback.core.sift.SiftProcessor@368ec75c - End of configuration. [testng] [2024-11-20 01:09:36,393] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-11-20 01:09:45,244] [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] [2024-11-20 01:09:46,467] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-11-20 01:09:47,505] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-11-20 01:09:48,463] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-11-20 01:09:51,396] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-11-20 01:09:55,515] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex: [testng] [2024-11-20 01:09:56,754] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-11-20 01:10:04,612] [pool-1-thread-5] Initializing /data/tony/test.tiff: [testng] [2024-11-20 01:10:07,070] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-11-20 01:10:15,610] [pool-1-thread-2] Initializing /data/tony/001001000_objects.flex: [testng] [2024-11-20 01:10:16,800] [pool-1-thread-1] Initializing /data/achim/003003000.flex: [testng] [2024-11-20 01:10:18,108] [pool-1-thread-4] Initializing /data/tamjid/006005000.flex: [testng] [2024-11-20 01:10:24,984] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] [2024-11-20 01:10:26,250] [pool-1-thread-11] Initializing /data/qa-18096/002003001.flex: [testng] [2024-11-20 01:10:28,980] [pool-1-thread-12] Initializing /data/anatole/001004000.flex: [testng] [2024-11-20 01:10:33,730] [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] [2024-11-20 01:10:36,499] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-11-20 01:10:46,050] [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] [2024-11-20 01:10:53,271] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-11-20 01:10:54,624] [pool-1-thread-1] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-11-20 01:11:00,313] [pool-1-thread-9] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-11-20 01:11:05,716] [pool-1-thread-5] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-11-20 01:11:12,435] [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] [2024-11-20 01:11:17,593] [pool-1-thread-2] Initializing /data/tony/015002000.tiff: [testng] [2024-11-20 01:11:22,103] [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] [2024-11-20 01:11:23,633] [pool-1-thread-11] Initializing /data/qa-17190/002002011.flex: [testng] [2024-11-20 01:11:33,928] [pool-1-thread-2] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-11-20 01:11:39,572] [pool-1-thread-11] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-11-20 01:12:03,036] [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: 22 minutes 28 seconds Finished: SUCCESS