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Started by upstream project "BIOFORMATS-test-repo" build number 392 originally caused by: Started by upstream project "Trigger" build number 416 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@12 [BIOFORMATS-test-folder@12] $ /bin/bash -xe /tmp/jenkins13132283994582517721.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61949_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 08:06:24,915 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 08:06:24,916 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 08:06:24,916 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:06:24,917 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:06:24,918 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:06:24,918 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:06:24,918 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 08:06:24,918 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:06:24,919 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:06:24,920 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:06:24,920 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:06:24,920 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:06:25,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:06:25,065 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:06:25,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:06:25,087 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:06:25,093 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:06:25,093 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:06:25,093 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:06:25,094 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:06:25,094 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration. [testng] 08:06:25,095 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point [testng] 08:06:25,095 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 176 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-27 08:06:25,103] [main] java.version = 21 [testng] 08:06:25,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:06:25,106 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:06:25,145 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-27_08-06-25.log] [testng] 08:06:25,146 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-03-27 08:06:25,147] [main] testng.directory = /data [testng] [2025-03-27 08:06:25,148] [main] testng.configDirectory = /config [testng] [2025-03-27 08:06:25,156] [main] testng.multiplier = 1.0 [testng] [2025-03-27 08:06:25,156] [main] testng.in-memory = false [testng] [2025-03-27 08:06:25,156] [main] testng.allow-missing = false [testng] [2025-03-27 08:06:25,156] [main] user.language = en [testng] [2025-03-27 08:06:25,156] [main] user.country = ${user.country} [testng] [2025-03-27 08:06:25,156] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-27 08:16:51,952] [main] ---------------------------------------- [testng] [2025-03-27 08:16:51,953] [main] Total files: 46 [testng] [2025-03-27 08:16:51,953] [main] Scan time: 626.795 s (13625 ms/file) [testng] [2025-03-27 08:16:51,953] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-27 08:43:49,569] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 08:43:49,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 08:43:49,570 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:43:49,571 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-27_08-43-49.log] [testng] 08:43:49,572 |-INFO in ch.qos.logback.core.sift.SiftProcessor@349fd51 - End of configuration. [testng] [2025-03-27 08:44:26,675] [pool-1-thread-12] Initializing /data/samples/fibre.vws: [testng] 08:44:26,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 08:44:26,675 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:44:26,676 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-27_08-44-26.log] [testng] 08:44:26,676 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4eab00b7 - End of configuration. [testng] [2025-03-27 08:45:00,954] [pool-1-thread-11] Initializing /data/andreas/090812E4.vws: [testng] 08:45:00,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 08:45:00,954 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:45:00,955 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-27_08-45-00.log] [testng] 08:45:00,955 |-INFO in ch.qos.logback.core.sift.SiftProcessor@c2cbd1e - End of configuration. [testng] [2025-03-27 08:46:32,773] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 08:46:32,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 08:46:32,774 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:46:32,775 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-27_08-46-32.log] [testng] 08:46:32,775 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1bce8fab - End of configuration. [testng] [2025-03-27 08:47:07,267] [pool-1-thread-9] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 08:47:07,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 08:47:07,267 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:47:07,268 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-27_08-47-07.log] [testng] 08:47:07,269 |-INFO in ch.qos.logback.core.sift.SiftProcessor@72df112a - End of configuration. [testng] [2025-03-27 08:48:28,671] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 08:48:28,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 08:48:28,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:48:28,671 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-27_08-48-28.log] [testng] 08:48:28,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27c23bfe - End of configuration. [testng] [2025-03-27 08:48:59,459] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 08:48:59,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 08:48:59,459 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:48:59,459 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-27_08-48-59.log] [testng] 08:48:59,460 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3424afd6 - End of configuration. [testng] [2025-03-27 08:49:38,586] [pool-1-thread-6] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 08:49:38,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 08:49:38,586 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:49:38,587 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-27_08-49-38.log] [testng] 08:49:38,587 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32f18ab0 - End of configuration. [testng] [2025-03-27 08:51:01,689] [pool-1-thread-5] Initializing /data/stephan/two sequences.vws: [testng] 08:51:01,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 08:51:01,689 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:01,690 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-27_08-51-01.log] [testng] 08:51:01,690 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7932e1ab - End of configuration. [testng] [2025-03-27 08:51:22,321] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] 08:51:22,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 08:51:22,322 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:51:22,322 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-27_08-51-22.log] [testng] 08:51:22,323 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22e9269 - End of configuration. [testng] [2025-03-27 08:52:01,572] [pool-1-thread-3] Initializing /data/andreas/090811E1.vws: [testng] 08:52:01,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 08:52:01,572 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:52:01,573 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-27_08-52-01.log] [testng] 08:52:01,573 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5ec4944 - End of configuration. [testng] [2025-03-27 08:55:29,511] [pool-1-thread-2] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 08:55:29,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 08:55:29,511 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:55:29,512 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-27_08-55-29.log] [testng] 08:55:29,512 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75dfbc66 - End of configuration. [testng] [2025-03-27 09:02:35,633] [pool-1-thread-12] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2025-03-27 09:05:15,768] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2025-03-27 09:07:09,904] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2025-03-27 09:16:50,141] [pool-1-thread-1] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-03-27 09:18:02,290] [pool-1-thread-6] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2025-03-27 09:20:43,108] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2025-03-27 09:32:05,240] [pool-1-thread-4] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2025-03-27 09:34:44,133] [pool-1-thread-8] Initializing /data/imagesc-84715/not working.vws: [testng] [2025-03-27 09:35:42,299] [pool-1-thread-7] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2025-03-27 09:42:59,294] [pool-1-thread-12] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2025-03-27 09:50:46,089] [pool-1-thread-5] Initializing /data/gerhard/test.vws: [testng] [2025-03-27 09:51:24,011] [pool-1-thread-10] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2025-03-27 10:01:38,606] [pool-1-thread-5] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] 10:06:13,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:06:13,211 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:06:13,212 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-27_10-06-13.log] [testng] 10:06:13,212 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45079391 - End of configuration. [testng] 11:32:35,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 11:32:35,847 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:32:35,848 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-27_11-32-35.log] [testng] 11:32:35,849 |-INFO in ch.qos.logback.core.sift.SiftProcessor@641e7e04 - End of configuration. [testng] 11:39:58,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 11:39:58,220 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 11:39:58,221 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-27_11-39-58.log] [testng] 11:39:58,221 |-INFO in ch.qos.logback.core.sift.SiftProcessor@123e12de - End of configuration. [testng] 14:53:02,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 14:53:02,631 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 14:53:02,632 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-27_14-53-02.log] [testng] 14:53:02,633 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47096b52 - End of configuration. Build was aborted Calling Pipeline was cancelled Finished: ABORTED