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Started by upstream project "BIOFORMATS-test-repo" build number 250 originally caused by: Started by upstream project "Trigger" build number 274 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@7 [BIOFORMATS-test-folder@7] $ /bin/bash -xe /tmp/jenkins3989938854905869992.sh + '[' flex = slidebook ']' ++ date +%u + '[' 6 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39373_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] 01:02:16,241 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:02:16,243 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - No custom configurators were discovered as a service. [testng] 01:02:16,243 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:02:16,244 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:02:16,245 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:02:16,245 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:02:16,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:02:16,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:02:16,246 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:02:16,247 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:02:16,247 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:02:16,248 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:02:16,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:02:16,433 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:02:16,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:02:16,460 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:02:16,466 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:02:16,466 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:02:16,466 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:02:16,467 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:02:16,467 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@45099dd3 - End of configuration. [testng] 01:02:16,468 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@60099951 - Registering current configuration as safe fallback point [testng] 01:02:16,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@65f095f8 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 222 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-09 01:02:16,477] [main] java.version = 11.0.16 [testng] 01:02:16,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:02:16,480 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:02:16,524 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-09_01-02-16.log] [testng] 01:02:16,526 |-INFO in ch.qos.logback.core.sift.SiftProcessor@21be3395 - End of configuration. [testng] [2024-11-09 01:02:16,529] [main] testng.directory = /data [testng] [2024-11-09 01:02:16,529] [main] testng.configDirectory = /config [testng] [2024-11-09 01:02:16,541] [main] testng.multiplier = 1.0 [testng] [2024-11-09 01:02:16,543] [main] testng.in-memory = false [testng] [2024-11-09 01:02:16,543] [main] testng.allow-missing = false [testng] [2024-11-09 01:02:16,543] [main] user.language = en [testng] [2024-11-09 01:02:16,543] [main] user.country = ${user.country} [testng] [2024-11-09 01:02:16,543] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-09 01:04:29,495] [main] ---------------------------------------- [testng] [2024-11-09 01:04:29,495] [main] Total files: 791 [testng] [2024-11-09 01:04:29,496] [main] Scan time: 132.952 s (168 ms/file) [testng] [2024-11-09 01:04:29,496] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 42 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-09 01:11:02,198] [pool-1-thread-1] Initializing /data/lee/RLM1 SSN3 300308 008015000.flex: [testng] 01:11:02,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:11:02,199 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:02,201 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-09_01-11-02.log] [testng] 01:11:02,202 |-INFO in ch.qos.logback.core.sift.SiftProcessor@b509ac6 - End of configuration. [testng] [2024-11-09 01:11:03,050] [pool-1-thread-12] Initializing /data/qa-18096/002003001.flex: [testng] 01:11:03,050 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:11:03,051 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:03,052 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-09_01-11-03.log] [testng] 01:11:03,053 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6daaa1e3 - End of configuration. [testng] [2024-11-09 01:11:03,960] [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] 01:11:03,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:11:03,960 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:03,961 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-09_01-11-03.log] [testng] 01:11:03,962 |-INFO in ch.qos.logback.core.sift.SiftProcessor@17bfc999 - End of configuration. [testng] [2024-11-09 01:11:04,951] [pool-1-thread-10] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement1_6fields/Meas_01(2007-12-13_17-19-36)/004006000.flex: [testng] 01:11:04,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:11:04,952 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:04,953 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-09_01-11-04.log] [testng] 01:11:04,953 |-INFO in ch.qos.logback.core.sift.SiftProcessor@546602f4 - End of configuration. [testng] [2024-11-09 01:11:06,033] [pool-1-thread-9] Initializing /data/public/idr0001/X_110331_S13/Meas_04(2011-03-31_13-55-29)/001002000.flex: [testng] 01:11:06,033 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:11:06,034 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:06,034 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-09_01-11-06.log] [testng] 01:11:06,034 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11f6de2d - End of configuration. [testng] [2024-11-09 01:11:13,669] [pool-1-thread-8] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071213_measurement2_stack/Meas_01(2007-12-13_17-49-27)/004006000.flex: [testng] 01:11:13,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:11:13,670 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:13,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-09_01-11-13.log] [testng] 01:11:13,671 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69789244 - End of configuration. [testng] [2024-11-09 01:11:14,837] [pool-1-thread-7] Initializing /data/tony/003008000.flex: [testng] 01:11:14,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:11:14,837 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:14,838 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-09_01-11-14.log] [testng] 01:11:14,838 |-INFO in ch.qos.logback.core.sift.SiftProcessor@26ac7de0 - End of configuration. [testng] [2024-11-09 01:11:16,275] [pool-1-thread-6] Initializing /data/tony/003003000.tiff: [testng] 01:11:16,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:11:16,275 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:16,276 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-09_01-11-16.log] [testng] 01:11:16,277 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ec5dacf - End of configuration. [testng] [2024-11-09 01:11:18,503] [pool-1-thread-5] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_03(2007-12-14_10-50-56)/004006000.flex: [testng] 01:11:18,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:11:18,503 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:18,504 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-09_01-11-18.log] [testng] 01:11:18,505 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f22d9d0 - End of configuration. [testng] [2024-11-09 01:11:19,569] [pool-1-thread-4] Initializing /data/qa-2983/004007000.flex: [testng] 01:11:19,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:11:19,569 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:19,570 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-09_01-11-19.log] [testng] 01:11:19,570 |-INFO in ch.qos.logback.core.sift.SiftProcessor@52e9ac00 - End of configuration. [testng] [2024-11-09 01:11:20,605] [pool-1-thread-3] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_06(2007-12-14_11-50-57)/004006000.flex: [testng] 01:11:20,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:11:20,605 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:20,606 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-09_01-11-20.log] [testng] 01:11:20,606 |-INFO in ch.qos.logback.core.sift.SiftProcessor@755746a5 - End of configuration. [testng] [2024-11-09 01:11:22,268] [pool-1-thread-2] Initializing /data/tony/000101400 - from PE sofwatre.tif: [testng] 01:11:22,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:11:22,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:11:22,269 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-09_01-11-22.log] [testng] 01:11:22,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@ebb436c - End of configuration. [testng] [2024-11-09 01:11:38,935] [pool-1-thread-2] Initializing /data/anatole/001004000.flex: [testng] [2024-11-09 01:11:40,769] [pool-1-thread-6] Initializing /data/qa-18096/002002001.flex: [testng] [2024-11-09 01:11:41,963] [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] [2024-11-09 01:11:43,075] [pool-1-thread-4] Initializing /data/tony/test1.flex: [testng] [2024-11-09 01:11:44,204] [pool-1-thread-1] Initializing /data/stephane/002007000.flex: [testng] [2024-11-09 01:11:51,040] [pool-1-thread-11] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_07(2007-12-14_12-20-57)/004006000.flex: [testng] [2024-11-09 01:11:52,301] [pool-1-thread-5] Initializing /data/qa-7469/002002.flex: [testng] [2024-11-09 01:11:53,414] [pool-1-thread-8] Initializing /data/tony/001014000 - from flex.tif: [testng] [2024-11-09 01:11:55,571] [pool-1-thread-7] Initializing /data/anatole/Meas_05(2012-05-16_18-51-33)/001009001.flex: [testng] [2024-11-09 01:12:05,124] [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] [2024-11-09 01:12:06,413] [pool-1-thread-4] Initializing /data/public/idr0001/X_110331_S13/Meas_03(2011-03-31_13-14-40)/001001000.flex: [testng] [2024-11-09 01:12:15,888] [pool-1-thread-1] Initializing /data/ghislain/test.flex: [testng] [2024-11-09 01:12:18,863] [pool-1-thread-12] Initializing /data/tamjid/006005000.flex: [testng] [2024-11-09 01:12:20,406] [pool-1-thread-10] Initializing /data/public/idr0001/X_110331_S13/Meas_05(2011-03-31_14-36-06)/001001000.flex: [testng] [2024-11-09 01:12:32,110] [pool-1-thread-5] Initializing /data/public/idr0001/X_110331_S13/Meas_06(2011-03-31_15-16-53)/001001000.flex: [testng] [2024-11-09 01:12:42,968] [pool-1-thread-8] Initializing /data/manuel/003003001.flex: [testng] [2024-11-09 01:12:47,994] [pool-1-thread-11] Initializing /data/public/idr0007/Plate1/001001000.flex: [testng] [2024-11-09 01:13:01,252] [pool-1-thread-2] Initializing /data/stephane/006013000.flex: [testng] [2024-11-09 01:13:05,880] [pool-1-thread-3] Initializing /data/tony/015002000.tiff: [testng] [2024-11-09 01:13:08,700] [pool-1-thread-12] Initializing /data/christophe/B5_1 GFP RFP Draq5 20times 7planes step2.flex: [testng] [2024-11-09 01:13:10,167] [pool-1-thread-1] Initializing /data/karsten/BioFormats_FLEX181_PKI/AFo_071214_measurement3_kinetics_10x/Meas_04(2007-12-14_11-05-56)/004006000.flex: [testng] [2024-11-09 01:13:11,608] [pool-1-thread-6] Initializing /data/tony/test.tiff: [testng] [2024-11-09 01:13:28,780] [pool-1-thread-8] Initializing /data/tamjid/006003000.flex: [testng] [2024-11-09 01:13:30,186] [pool-1-thread-6] Initializing /data/public/idr0001/X_110331_S13/Meas_02(2011-03-31_12-33-53)/001001000.flex: [testng] [2024-11-09 01:13:41,628] [pool-1-thread-3] Initializing /data/public/idr0001/X_110331_S13/Meas_01(2011-03-31_11-53-03)/001001000.flex: [testng] [2024-11-09 01:13:57,237] [pool-1-thread-2] Initializing /data/qa-17190/002002011.flex: [testng] [2024-11-09 01:14:00,365] [pool-1-thread-1] Initializing /data/tony/001001000_objects.flex: [testng] [2024-11-09 01:14:10,317] [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] [2024-11-09 01:14:14,215] [pool-1-thread-7] Initializing /data/achim/003003000.flex: [testng] [2024-11-09 01:14:17,366] [pool-1-thread-2] Initializing /data/tamjid/006004000.flex: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 2226, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 23 minutes 12 seconds Finished: SUCCESS