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Started by upstream project "BIOFORMATS-test-repo" build number 361 originally caused by: Started by upstream project "Trigger" build number 387 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins1600458259138983385.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_57525_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] WARNING: An illegal reflective access operation has occurred [testng] WARNING: Illegal reflective access by org.kohsuke.file_leak_detector.Listener (file:/home/build/.m2/repository/org/kohsuke/file-leak-detector/1.18/file-leak-detector-1.18-jar-with-dependencies.jar) to field java.net.SocketImpl.socket [testng] WARNING: Please consider reporting this to the maintainers of org.kohsuke.file_leak_detector.Listener [testng] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [testng] WARNING: All illegal access operations will be denied in a future release [testng] File leak detector installed [testng] 00:47:08,992 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:47:08,993 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 00:47:08,993 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:47:08,994 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:47:08,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:47:08,995 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:47:08,996 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:47:08,996 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:47:08,996 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:47:08,997 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:47:08,997 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:47:08,997 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:47:09,168 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:47:09,169 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:47:09,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:47:09,191 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:47:09,197 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:47:09,197 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:47:09,197 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:47:09,198 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:47:09,198 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 00:47:09,198 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 00:47:09,198 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 202 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-01 00:47:09,208] [main] java.version = 11.0.16 [testng] 00:47:09,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:47:09,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:47:09,253 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-01_00-47-09.log] [testng] 00:47:09,255 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-01 00:47:09,257] [main] testng.directory = /data [testng] [2025-03-01 00:47:09,257] [main] testng.configDirectory = /config [testng] [2025-03-01 00:47:09,267] [main] testng.multiplier = 1.0 [testng] [2025-03-01 00:47:09,268] [main] testng.in-memory = false [testng] [2025-03-01 00:47:09,269] [main] testng.allow-missing = false [testng] [2025-03-01 00:47:09,269] [main] user.language = en [testng] [2025-03-01 00:47:09,269] [main] user.country = ${user.country} [testng] [2025-03-01 00:47:09,269] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-01 00:47:38,028] [main] ---------------------------------------- [testng] [2025-03-01 00:47:38,029] [main] Total files: 791 [testng] [2025-03-01 00:47:38,029] [main] Scan time: 28.759 s (36 ms/file) [testng] [2025-03-01 00:47:38,029] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-01 00:52:21,357] [pool-1-thread-1] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] 00:52:21,357 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:52:21,358 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:21,359 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-01_00-52-21.log] [testng] 00:52:21,360 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7a050ed4 - End of configuration. [testng] [2025-03-01 00:52:25,495] [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] 00:52:25,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:52:25,495 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:25,497 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-01_00-52-25.log] [testng] 00:52:25,497 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7881f0be - End of configuration. [testng] [2025-03-01 00:52:26,040] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 00:52:26,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:52:26,041 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:26,041 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-01_00-52-26.log] [testng] 00:52:26,042 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17d38308 - End of configuration. [testng] [2025-03-01 00:52:27,206] [pool-1-thread-10] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 00:52:27,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:52:27,206 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:27,207 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-01_00-52-27.log] [testng] 00:52:27,207 |-INFO in ch.qos.logback.core.sift.SiftProcessor@522d8a85 - End of configuration. [testng] [2025-03-01 00:52:27,762] [pool-1-thread-9] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] 00:52:27,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:52:27,762 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:27,763 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-01_00-52-27.log] [testng] 00:52:27,763 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ef33d0d - End of configuration. [testng] [2025-03-01 00:52:28,493] [pool-1-thread-8] Initializing /data/qa-7469/002002.flex: [testng] 00:52:28,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:52:28,493 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:28,494 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-01_00-52-28.log] [testng] 00:52:28,494 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77adb662 - End of configuration. [testng] [2025-03-01 00:52:29,077] [pool-1-thread-7] Initializing /data/ghislain/test.flex: [testng] 00:52:29,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:52:29,077 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:29,078 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-01_00-52-29.log] [testng] 00:52:29,078 |-INFO in ch.qos.logback.core.sift.SiftProcessor@571274db - End of configuration. [testng] [2025-03-01 00:52:29,640] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] 00:52:29,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:52:29,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:29,641 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-01_00-52-29.log] [testng] 00:52:29,642 |-INFO in ch.qos.logback.core.sift.SiftProcessor@70320595 - End of configuration. [testng] [2025-03-01 00:52:30,581] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 00:52:30,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:52:30,581 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:30,582 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-01_00-52-30.log] [testng] 00:52:30,582 |-INFO in ch.qos.logback.core.sift.SiftProcessor@54deca03 - End of configuration. [testng] [2025-03-01 00:52:35,436] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 00:52:35,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:52:35,436 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:35,437 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-01_00-52-35.log] [testng] 00:52:35,437 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c2bd05d - End of configuration. [testng] [2025-03-01 00:52:36,118] [pool-1-thread-3] Initializing /data/tony/001001000_objects.flex: [testng] 00:52:36,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:52:36,118 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:36,119 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-01_00-52-36.log] [testng] 00:52:36,119 |-INFO in ch.qos.logback.core.sift.SiftProcessor@416f3ee4 - End of configuration. [testng] [2025-03-01 00:52:36,827] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 00:52:36,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:52:36,827 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:52:36,828 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-01_00-52-36.log] [testng] 00:52:36,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7eaa8ab - End of configuration. [testng] [2025-03-01 00:52:52,306] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] [2025-03-01 00:52:53,339] [pool-1-thread-8] Initializing /data/tamjid/006005000.flex: [testng] [2025-03-01 00:52:54,368] [pool-1-thread-10] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2025-03-01 00:52:55,665] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2025-03-01 00:53:02,607] [pool-1-thread-7] Initializing /data/tony/003003000.tiff: [testng] [2025-03-01 00:53:05,959] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2025-03-01 00:53:13,516] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2025-03-01 00:53:14,514] [pool-1-thread-4] Initializing /data/tony/001014000 - from flex.tif: [testng] [2025-03-01 00:53:16,470] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2025-03-01 00:53:30,310] [pool-1-thread-8] Initializing /data/qa-2983/004007000.flex: [testng] [2025-03-01 00:53:32,947] [pool-1-thread-7] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2025-03-01 00:53:35,912] [pool-1-thread-4] Initializing /data/anatole/001004000.flex: [testng] [2025-03-01 00:53:42,801] [pool-1-thread-12] Initializing /data/tony/test1.flex: [testng] [2025-03-01 00:53:43,781] [pool-1-thread-8] Initializing /data/stephane/002007000.flex: [testng] [2025-03-01 00:53:44,825] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2025-03-01 00:53:58,307] [pool-1-thread-12] Initializing /data/qa-17190/002002011.flex: [testng] [2025-03-01 00:53:59,171] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2025-03-01 00:54:07,629] [pool-1-thread-11] Initializing /data/tony/003008000.flex: [testng] [2025-03-01 00:54:11,550] [pool-1-thread-12] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] [2025-03-01 00:54:12,670] [pool-1-thread-8] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2025-03-01 00:54:24,248] [pool-1-thread-4] Initializing /data/tony/015002000.tiff: [testng] [2025-03-01 00:54:35,862] [pool-1-thread-7] Initializing /data/qa-18096/002003001.flex: [testng] [2025-03-01 00:54:36,929] [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] [2025-03-01 00:54:39,567] [pool-1-thread-4] Initializing /data/qa-18096/002002001.flex: [testng] [2025-03-01 00:54:40,648] [pool-1-thread-12] Initializing /data/achim/003003000.flex: [testng] [2025-03-01 00:54:52,537] [pool-1-thread-7] Initializing /data/tamjid/006004000.flex: [testng] [2025-03-01 00:54:54,384] [pool-1-thread-10] Initializing /data/manuel/003003001.flex: [testng] [2025-03-01 00:54:56,492] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_02(2007-12-14_10-40-56)/004006000.flex: [testng] [2025-03-01 00:55:02,137] [pool-1-thread-11] Initializing /data/tony/test.tiff: [testng] [2025-03-01 00:55:04,106] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 13 minutes 28 seconds Finished: SUCCESS