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Started by upstream project "BIOFORMATS-test-repo" build number 206 originally caused by: Started by upstream project "Trigger" build number 232 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@9 [BIOFORMATS-test-folder@9] $ /bin/bash -xe /tmp/jenkins1970282005611055053.sh + '[' flex = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_32673_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] 01:42:52,642 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:42:52,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - No custom configurators were discovered as a service. [testng] 01:42:52,644 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:42:52,645 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:42:52,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:42:52,646 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:42:52,646 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:42:52,646 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:42:52,647 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:42:52,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:42:52,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:42:52,648 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:42:52,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:42:52,836 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:42:52,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:42:52,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:42:52,868 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:42:52,869 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:42:52,869 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:42:52,869 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:42:52,869 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2794eab6 - End of configuration. [testng] 01:42:52,870 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6c1a5b54 - Registering current configuration as safe fallback point [testng] 01:42:52,870 |-INFO in ch.qos.logback.classic.util.ContextInitializer@3a6bb9bf - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 223 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-01 01:42:52,881] [main] java.version = 11.0.16 [testng] 01:42:52,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:42:52,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:42:52,936 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-01_01-42-52.log] [testng] 01:42:52,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@642a7222 - End of configuration. [testng] [2024-10-01 01:42:52,940] [main] testng.directory = /data [testng] [2024-10-01 01:42:52,941] [main] testng.configDirectory = /config [testng] [2024-10-01 01:42:52,954] [main] testng.multiplier = 1.0 [testng] [2024-10-01 01:42:52,956] [main] testng.in-memory = false [testng] [2024-10-01 01:42:52,956] [main] testng.allow-missing = false [testng] [2024-10-01 01:42:52,956] [main] user.language = en [testng] [2024-10-01 01:42:52,956] [main] user.country = ${user.country} [testng] [2024-10-01 01:42:52,956] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-01 01:43:40,176] [main] ---------------------------------------- [testng] [2024-10-01 01:43:40,177] [main] Total files: 791 [testng] [2024-10-01 01:43:40,177] [main] Scan time: 47.22 s (59 ms/file) [testng] [2024-10-01 01:43:40,177] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-01 01:49:07,525] [pool-1-thread-1] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] 01:49:07,526 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:49:07,527 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:07,528 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-01_01-49-07.log] [testng] 01:49:07,529 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36ecee25 - End of configuration. [testng] [2024-10-01 01:49:11,104] [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] 01:49:11,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:49:11,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-01_01-49-11.log] [testng] 01:49:11,105 |-INFO in ch.qos.logback.core.sift.SiftProcessor@12a7bbd5 - End of configuration. [testng] [2024-10-01 01:49:11,488] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_01(2007-12-14_10-35-55)/004006000.flex: [testng] 01:49:11,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:49:11,488 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,489 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-01_01-49-11.log] [testng] 01:49:11,489 |-INFO in ch.qos.logback.core.sift.SiftProcessor@95537a6 - End of configuration. [testng] [2024-10-01 01:49:11,945] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] 01:49:11,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:49:11,945 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:11,946 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-01_01-49-11.log] [testng] 01:49:11,946 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c6144fa - End of configuration. [testng] [2024-10-01 01:49:15,563] [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] 01:49:15,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:49:15,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:15,564 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-01_01-49-15.log] [testng] 01:49:15,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5d4150ae - End of configuration. [testng] [2024-10-01 01:49:16,090] [pool-1-thread-8] Initializing /data/tony/test.tiff: [testng] 01:49:16,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:49:16,090 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:16,090 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-01_01-49-16.log] [testng] 01:49:16,091 |-INFO in ch.qos.logback.core.sift.SiftProcessor@d17e63e - End of configuration. [testng] [2024-10-01 01:49:17,050] [pool-1-thread-7] Initializing /data/tony/015002000.tiff: [testng] 01:49:17,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:49:17,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:17,051 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-01_01-49-17.log] [testng] 01:49:17,052 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2d8ba2e2 - End of configuration. [testng] [2024-10-01 01:49:17,947] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_05(2007-12-14_11-25-56)/004006000.flex: [testng] 01:49:17,947 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:49:17,948 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:17,948 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-01_01-49-17.log] [testng] 01:49:17,949 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6612fd18 - End of configuration. [testng] [2024-10-01 01:49:18,387] [pool-1-thread-5] Initializing /data/anatole/001004000.flex: [testng] 01:49:18,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:49:18,388 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:18,388 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-01_01-49-18.log] [testng] 01:49:18,388 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22b7427d - End of configuration. [testng] [2024-10-01 01:49:19,049] [pool-1-thread-4] Initializing /data/stephane/002007000.flex: [testng] 01:49:19,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:49:19,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:19,050 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-01_01-49-19.log] [testng] 01:49:19,050 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43d5ddde - End of configuration. [testng] [2024-10-01 01:49:19,499] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_08(2007-12-14_12-55-57)/004006000.flex: [testng] 01:49:19,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:49:19,499 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:19,500 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-01_01-49-19.log] [testng] 01:49:19,500 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21f9b8de - End of configuration. [testng] [2024-10-01 01:49:20,018] [pool-1-thread-2] Initializing /data/tony/001014000 - from flex.tif: [testng] 01:49:20,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:49:20,018 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:49:20,019 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-01_01-49-20.log] [testng] 01:49:20,019 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2998224 - End of configuration. [testng] [2024-10-01 01:49:27,973] [pool-1-thread-2] Initializing /data/qa-7469/002002.flex: [testng] [2024-10-01 01:49:28,510] [pool-1-thread-7] Initializing /data/qa-2983/004007000.flex: [testng] [2024-10-01 01:49:28,983] [pool-1-thread-8] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-10-01 01:49:29,773] [pool-1-thread-4] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-10-01 01:49:32,993] [pool-1-thread-6] Initializing /data/tamjid/006003000.flex: [testng] [2024-10-01 01:49:33,394] [pool-1-thread-9] Initializing /data/tony/003008000.flex: [testng] [2024-10-01 01:49:33,878] [pool-1-thread-3] Initializing /data/ghislain/test.flex: [testng] [2024-10-01 01:49:34,291] [pool-1-thread-11] Initializing /data/stephane/006013000.flex: [testng] [2024-10-01 01:49:34,770] [pool-1-thread-12] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] [2024-10-01 01:49:37,597] [pool-1-thread-2] Initializing /data/manuel/003003001.flex: [testng] [2024-10-01 01:49:38,123] [pool-1-thread-7] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-10-01 01:49:44,624] [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] [2024-10-01 01:49:45,274] [pool-1-thread-4] Initializing /data/tony/001001000_objects.flex: [testng] [2024-10-01 01:49:46,215] [pool-1-thread-3] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-10-01 01:49:51,158] [pool-1-thread-12] Initializing /data/qa-17190/002002011.flex: [testng] [2024-10-01 01:49:51,795] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-10-01 01:50:00,226] [pool-1-thread-9] Initializing /data/qa-18096/002002001.flex: [testng] [2024-10-01 01:50:03,169] [pool-1-thread-11] Initializing /data/tamjid/006004000.flex: [testng] [2024-10-01 01:50:04,816] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2024-10-01 01:50:06,368] [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] [2024-10-01 01:50:09,048] [pool-1-thread-6] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] [2024-10-01 01:50:10,395] [pool-1-thread-9] Initializing /data/tamjid/006005000.flex: [testng] [2024-10-01 01:50:11,123] [pool-1-thread-2] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] [2024-10-01 01:50:17,751] [pool-1-thread-11] Initializing /data/achim/003003000.flex: [testng] [2024-10-01 01:50:21,472] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-10-01 01:50:31,219] [pool-1-thread-9] Initializing /data/qa-18096/002003001.flex: [testng] [2024-10-01 01:50:37,557] [pool-1-thread-11] Initializing /data/tony/003003000.tiff: [testng] [2024-10-01 01:50:41,778] [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] [2024-10-01 01:50:45,071] [pool-1-thread-12] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-10-01 01:50:48,539] [pool-1-thread-11] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 15 minutes 8 seconds Finished: SUCCESS