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Started by upstream project "BIOFORMATS-test-repo" build number 289 originally caused by: Started by upstream project "Trigger" build number 308 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@4 [BIOFORMATS-test-folder@4] $ /bin/bash -xe /tmp/jenkins999929602770106659.sh + '[' flex = slidebook ']' ++ date +%u + '[' 5 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45642_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 test-automated: [testng] File leak detector installed [testng] 01:48:11,449 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:48:11,451 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - No custom configurators were discovered as a service. [testng] 01:48:11,451 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:48:11,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:48:11,452 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:48:11,452 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:48:11,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 0 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:48:11,452 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:48:11,453 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:48:11,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:48:11,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:48:11,453 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:48:11,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:48:11,672 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:48:11,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:48:11,700 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:48:11,708 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:48:11,708 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:48:11,708 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:48:11,708 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:48:11,708 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@7a69b07 - End of configuration. [testng] 01:48:11,709 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@636be97c - Registering current configuration as safe fallback point [testng] 01:48:11,709 |-INFO in ch.qos.logback.classic.util.ContextInitializer@79ad8b2f - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 256 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-13 01:48:11,719] [main] java.version = 1.8.0_342 [testng] 01:48:11,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:48:11,722 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:11,766 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-13_01-48-11.log] [testng] 01:48:11,768 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13c9d689 - End of configuration. [testng] [2024-12-13 01:48:11,769] [main] testng.directory = /data [testng] [2024-12-13 01:48:11,770] [main] testng.configDirectory = /config [testng] [2024-12-13 01:48:11,782] [main] testng.multiplier = 1.0 [testng] [2024-12-13 01:48:11,782] [main] testng.in-memory = false [testng] [2024-12-13 01:48:11,782] [main] testng.allow-missing = false [testng] [2024-12-13 01:48:11,782] [main] user.language = en [testng] [2024-12-13 01:48:11,782] [main] user.country = ${user.country} [testng] [2024-12-13 01:48:11,782] [main] Maximum heap size = 13653 MB [testng] Scanning for files... [testng] [2024-12-13 01:51:37,985] [main] ---------------------------------------- [testng] [2024-12-13 01:51:37,985] [main] Total files: 791 [testng] [2024-12-13 01:51:37,985] [main] Scan time: 206.203 s (260 ms/file) [testng] [2024-12-13 01:51:37,985] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-13 02:01:15,318] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 02:01:15,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:01:15,319 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:15,319 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-13_02-01-15.log] [testng] 02:01:15,320 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c7ef8ab - End of configuration. [testng] [2024-12-13 02:01:18,465] [pool-1-thread-12] Initializing /data/tamjid/006004000.flex: [testng] 02:01:18,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:01:18,465 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:18,466 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-13_02-01-18.log] [testng] 02:01:18,466 |-INFO in ch.qos.logback.core.sift.SiftProcessor@38a3da3d - End of configuration. [testng] [2024-12-13 02:01:20,553] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 02:01:20,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:01:20,553 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:20,553 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-13_02-01-20.log] [testng] 02:01:20,554 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62ea3b46 - End of configuration. [testng] [2024-12-13 02:01:23,002] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] 02:01:23,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:01:23,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:23,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-13_02-01-23.log] [testng] 02:01:23,003 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29443761 - End of configuration. [testng] [2024-12-13 02:01:25,656] [pool-1-thread-9] Initializing /data/stephane/006013000.flex: [testng] 02:01:25,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:01:25,656 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:25,657 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-13_02-01-25.log] [testng] 02:01:25,657 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ad352f - End of configuration. [testng] [2024-12-13 02:01:28,239] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 02:01:28,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:01:28,240 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:28,240 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-13_02-01-28.log] [testng] 02:01:28,241 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b8a7980 - End of configuration. [testng] [2024-12-13 02:01:30,703] [pool-1-thread-7] Initializing /data/qa-17190/002002011.flex: [testng] 02:01:30,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:01:30,703 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:30,704 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-13_02-01-30.log] [testng] 02:01:30,704 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6d4008dd - End of configuration. [testng] [2024-12-13 02:01:32,891] [pool-1-thread-6] Initializing /data/tony/001001000_objects.flex: [testng] 02:01:32,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:01:32,891 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:32,892 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-13_02-01-32.log] [testng] 02:01:32,892 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7ce00860 - End of configuration. [testng] [2024-12-13 02:01:35,539] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] 02:01:35,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:01:35,540 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:35,540 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-13_02-01-35.log] [testng] 02:01:35,540 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e21a2f3 - End of configuration. [testng] [2024-12-13 02:01:50,054] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 02:01:50,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:01:50,055 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:01:50,055 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-13_02-01-50.log] [testng] 02:01:50,055 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5a7462c - End of configuration. [testng] [2024-12-13 02:02:08,861] [pool-1-thread-3] Initializing /data/tony/001014000 - from flex.tif: [testng] 02:02:08,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:02:08,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:02:08,862 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-13_02-02-08.log] [testng] 02:02:08,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3622d3e0 - End of configuration. [testng] [2024-12-13 02:02:16,663] [pool-1-thread-2] Initializing /data/tony/test.tiff: [testng] 02:02:16,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:02:16,664 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:02:16,664 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-13_02-02-16.log] [testng] 02:02:16,665 |-INFO in ch.qos.logback.core.sift.SiftProcessor@23bfe909 - End of configuration. [testng] [2024-12-13 02:02:54,993] [pool-1-thread-3] Initializing /data/qa-2983/004007000.flex: [testng] [2024-12-13 02:02:57,328] [pool-1-thread-7] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-12-13 02:03:15,753] [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] [2024-12-13 02:03:19,927] [pool-1-thread-2] Initializing /data/ghislain/test.flex: [testng] [2024-12-13 02:03:22,931] [pool-1-thread-6] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [2024-12-13 02:03:51,319] [pool-1-thread-1] Initializing /data/tony/test1.flex: [testng] [2024-12-13 02:03:53,928] [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] [2024-12-13 02:03:57,317] [pool-1-thread-9] Initializing /data/qa-7469/002002.flex: [testng] [2024-12-13 02:03:59,897] [pool-1-thread-11] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-12-13 02:04:26,227] [pool-1-thread-6] Initializing /data/achim/003003000.flex: [testng] [2024-12-13 02:04:30,342] [pool-1-thread-10] Initializing /data/qa-18096/002003001.flex: [testng] [2024-12-13 02:04:35,811] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-12-13 02:05:08,867] [pool-1-thread-2] Initializing /data/tony/015002000.tiff: [testng] [2024-12-13 02:05:41,403] [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] [2024-12-13 02:05:45,150] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2024-12-13 02:05:52,468] [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] [2024-12-13 02:06:01,985] [pool-1-thread-2] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-12-13 02:06:05,111] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-12-13 02:06:20,983] [pool-1-thread-6] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-12-13 02:06:36,683] [pool-1-thread-9] Initializing /data/anatole/001004000.flex: [testng] [2024-12-13 02:06:39,921] [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] [2024-12-13 02:06:47,306] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-12-13 02:07:24,643] [pool-1-thread-12] Initializing /data/tamjid/006003000.flex: [testng] [2024-12-13 02:07:33,527] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-12-13 02:08:10,526] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-12-13 02:08:43,151] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2024-12-13 02:08:56,691] [pool-1-thread-12] Initializing /data/qa-18096/002002001.flex: [testng] [2024-12-13 02:09:25,451] [pool-1-thread-11] Initializing /data/tamjid/006005000.flex: [testng] [2024-12-13 02:09:28,841] [pool-1-thread-8] Initializing /data/tony/003003000.tiff: [testng] [2024-12-13 02:09:39,638] [pool-1-thread-9] Initializing /data/tony/003008000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 38 minutes 56 seconds Finished: SUCCESS