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Started by upstream project "BIOFORMATS-test-repo" build number 390 originally caused by: Started by upstream project "Trigger" build number 414 originally caused by: Started by user devspace Restarted from build #413, stage Bio-Formats Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@2 [BIOFORMATS-test-folder@2] $ /bin/bash -xe /tmp/jenkins9515037852523950144.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 2 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61726_merge_ci -v /uod/idr/repos/curated/tillvision:/data -v /uod/idr-scratch/merge-ci/curated/tillvision:/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] 01:44:15,507 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:44:15,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - No custom configurators were discovered as a service. [testng] 01:44:15,509 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:44:15,510 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:44:15,511 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:44:15,511 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:44:15,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:44:15,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:44:15,512 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:44:15,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:44:15,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:44:15,513 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:44:15,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:44:15,695 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:44:15,718 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:44:15,719 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:44:15,725 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:44:15,725 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:44:15,725 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:44:15,726 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:44:15,726 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@65c7a252 - End of configuration. [testng] 01:44:15,727 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@38cee291 - Registering current configuration as safe fallback point [testng] 01:44:15,727 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4d910fd6 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 215 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-25 01:44:15,737] [main] java.version = 11.0.16 [testng] 01:44:15,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:44:15,740 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:44:15,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-25_01-44-15.log] [testng] 01:44:15,788 |-INFO in ch.qos.logback.core.sift.SiftProcessor@13d73f29 - End of configuration. [testng] [2025-03-25 01:44:15,791] [main] testng.directory = /data [testng] [2025-03-25 01:44:15,791] [main] testng.configDirectory = /config [testng] [2025-03-25 01:44:15,803] [main] testng.multiplier = 1.0 [testng] [2025-03-25 01:44:15,805] [main] testng.in-memory = false [testng] [2025-03-25 01:44:15,806] [main] testng.allow-missing = false [testng] [2025-03-25 01:44:15,806] [main] user.language = en [testng] [2025-03-25 01:44:15,806] [main] user.country = ${user.country} [testng] [2025-03-25 01:44:15,806] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-25 01:45:07,903] [main] ---------------------------------------- [testng] [2025-03-25 01:45:07,903] [main] Total files: 46 [testng] [2025-03-25 01:45:07,903] [main] Scan time: 52.097 s (1132 ms/file) [testng] [2025-03-25 01:45:07,903] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-25 01:47:44,335] [pool-1-thread-1] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 01:47:44,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:47:44,336 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:44,338 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-25_01-47-44.log] [testng] 01:47:44,338 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29320ff - End of configuration. [testng] [2025-03-25 01:47:50,381] [pool-1-thread-12] Initializing /data/gerhard/test.vws: [testng] 01:47:50,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:47:50,381 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:50,382 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-25_01-47-50.log] [testng] 01:47:50,382 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66c92a37 - End of configuration. [testng] [2025-03-25 01:47:51,914] [pool-1-thread-11] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:47:51,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:47:51,914 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:51,914 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-25_01-47-51.log] [testng] 01:47:51,915 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4bb23c7b - End of configuration. [testng] [2025-03-25 01:47:57,673] [pool-1-thread-10] Initializing /data/andreas/090811E1.vws: [testng] 01:47:57,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:47:57,674 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:47:57,674 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-25_01-47-57.log] [testng] 01:47:57,675 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e93d9b7 - End of configuration. [testng] [2025-03-25 01:48:10,757] [pool-1-thread-9] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 01:48:10,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:48:10,757 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:10,758 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-25_01-48-10.log] [testng] 01:48:10,758 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349d1354 - End of configuration. [testng] [2025-03-25 01:48:12,394] [pool-1-thread-8] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 01:48:12,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:48:12,394 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:12,395 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-25_01-48-12.log] [testng] 01:48:12,395 |-INFO in ch.qos.logback.core.sift.SiftProcessor@48da454b - End of configuration. [testng] [2025-03-25 01:48:14,491] [pool-1-thread-7] Initializing /data/andreas/090812E4.vws: [testng] 01:48:14,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:48:14,491 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:14,492 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-25_01-48-14.log] [testng] 01:48:14,492 |-INFO in ch.qos.logback.core.sift.SiftProcessor@46eaab39 - End of configuration. [testng] [2025-03-25 01:48:20,117] [pool-1-thread-6] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 01:48:20,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:48:20,117 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:20,118 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-25_01-48-20.log] [testng] 01:48:20,118 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cc52d5d - End of configuration. [testng] [2025-03-25 01:48:26,061] [pool-1-thread-5] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:48:26,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:48:26,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:26,061 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-25_01-48-26.log] [testng] 01:48:26,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b86fc93 - End of configuration. [testng] [2025-03-25 01:48:28,058] [pool-1-thread-4] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:48:28,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:48:28,058 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:28,059 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-25_01-48-28.log] [testng] 01:48:28,059 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53131a4e - End of configuration. [testng] [2025-03-25 01:48:33,978] [pool-1-thread-3] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] 01:48:33,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:48:33,978 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:33,979 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-25_01-48-33.log] [testng] 01:48:33,979 |-INFO in ch.qos.logback.core.sift.SiftProcessor@77af5c53 - End of configuration. [testng] [2025-03-25 01:48:39,024] [pool-1-thread-2] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:48:39,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:48:39,024 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:48:39,025 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-25_01-48-39.log] [testng] 01:48:39,025 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6229c7bd - End of configuration. [testng] [2025-03-25 01:49:09,419] [pool-1-thread-12] Initializing /data/imagesc-84715/working.vws: [testng] [2025-03-25 01:49:19,218] [pool-1-thread-1] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2025-03-25 01:49:22,576] [pool-1-thread-4] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2025-03-25 01:49:25,372] [pool-1-thread-11] Initializing /data/stephan/two sequences.vws: [testng] [2025-03-25 01:49:27,730] [pool-1-thread-3] Initializing /data/samples/fibre.vws: [testng] [2025-03-25 01:49:48,823] [pool-1-thread-3] Initializing /data/imagesc-84715/not working.vws: [testng] [2025-03-25 01:49:56,109] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2025-03-25 01:50:38,391] [pool-1-thread-8] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-03-25 01:50:41,036] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2025-03-25 01:51:03,466] [pool-1-thread-12] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2025-03-25 01:51:13,120] [pool-1-thread-5] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] [2025-03-25 01:51:22,436] [pool-1-thread-3] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] [2025-03-25 01:51:37,090] [pool-1-thread-4] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 03:15:36,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 03:15:36,795 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 03:15:36,796 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-25_03-15-36.log] [testng] 03:15:36,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@476ee5b3 - End of configuration. [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 91 minutes 24 seconds Finished: SUCCESS