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Started by upstream project "BIOFORMATS-test-repo" build number 388 originally caused by: Started by upstream project "Trigger" build number 411 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@16 [BIOFORMATS-test-folder@16] $ /bin/bash -xe /tmp/jenkins16303444130347937459.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_61396_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] 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] 00:48:42,433 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 00:48:42,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - No custom configurators were discovered as a service. [testng] 00:48:42,434 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:42,435 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:48:42,435 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:48:42,436 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:48:42,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:48:42,436 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:42,437 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:48:42,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:48:42,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:48:42,437 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:48:42,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:48:42,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:48:42,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:48:42,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:48:42,628 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:48:42,628 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:48:42,628 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:48:42,628 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:48:42,629 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@3f6f6701 - End of configuration. [testng] 00:48:42,629 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@4f80542f - Registering current configuration as safe fallback point [testng] 00:48:42,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@2beee7ff - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 192 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-03-23 00:48:42,638] [main] java.version = 17.0.2 [testng] 00:48:42,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:48:42,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:48:42,679 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-03-23_00-48-42.log] [testng] 00:48:42,681 |-INFO in ch.qos.logback.core.sift.SiftProcessor@14bdbc74 - End of configuration. [testng] [2025-03-23 00:48:42,683] [main] testng.directory = /data [testng] [2025-03-23 00:48:42,683] [main] testng.configDirectory = /config [testng] [2025-03-23 00:48:42,698] [main] testng.multiplier = 1.0 [testng] [2025-03-23 00:48:42,698] [main] testng.in-memory = false [testng] [2025-03-23 00:48:42,698] [main] testng.allow-missing = false [testng] [2025-03-23 00:48:42,699] [main] user.language = en [testng] [2025-03-23 00:48:42,699] [main] user.country = ${user.country} [testng] [2025-03-23 00:48:42,699] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-03-23 00:49:07,460] [main] ---------------------------------------- [testng] [2025-03-23 00:49:07,460] [main] Total files: 46 [testng] [2025-03-23 00:49:07,460] [main] Scan time: 24.761 s (538 ms/file) [testng] [2025-03-23 00:49:07,460] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-03-23 00:50:34,993] [pool-1-thread-1] Initializing /data/andreas/090811E1.vws: [testng] 00:50:34,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:50:34,994 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:34,995 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-03-23_00-50-34.log] [testng] 00:50:34,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c27993d - End of configuration. [testng] [2025-03-23 00:50:44,659] [pool-1-thread-12] Initializing /data/gerhard/test.vws: [testng] 00:50:44,659 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:50:44,660 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:44,661 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-03-23_00-50-44.log] [testng] 00:50:44,661 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62659b24 - End of configuration. [testng] [2025-03-23 00:50:45,736] [pool-1-thread-11] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 00:50:45,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:50:45,736 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:45,737 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-03-23_00-50-45.log] [testng] 00:50:45,737 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1faa2417 - End of configuration. [testng] [2025-03-23 00:50:48,390] [pool-1-thread-10] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 00:50:48,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:50:48,390 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:48,390 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-03-23_00-50-48.log] [testng] 00:50:48,391 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f21614c - End of configuration. [testng] [2025-03-23 00:50:53,633] [pool-1-thread-9] Initializing /data/imagesc-84715/not working.vws: [testng] 00:50:53,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:50:53,634 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:53,634 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-03-23_00-50-53.log] [testng] 00:50:53,635 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2dd93b25 - End of configuration. [testng] [2025-03-23 00:50:54,648] [pool-1-thread-8] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] 00:50:54,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:50:54,648 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:54,649 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-03-23_00-50-54.log] [testng] 00:50:54,649 |-INFO in ch.qos.logback.core.sift.SiftProcessor@64386b11 - End of configuration. [testng] [2025-03-23 00:50:55,861] [pool-1-thread-7] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 00:50:55,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:50:55,862 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:55,862 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-03-23_00-50-55.log] [testng] 00:50:55,863 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1be1814c - End of configuration. [testng] [2025-03-23 00:50:58,919] [pool-1-thread-6] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 00:50:58,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:50:58,919 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:50:58,920 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-03-23_00-50-58.log] [testng] 00:50:58,920 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4dd62a96 - End of configuration. [testng] [2025-03-23 00:51:00,268] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 00:51:00,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:51:00,269 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:00,269 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-03-23_00-51-00.log] [testng] 00:51:00,270 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e4576c0 - End of configuration. [testng] [2025-03-23 00:51:01,230] [pool-1-thread-4] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 00:51:01,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:51:01,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:01,230 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-03-23_00-51-01.log] [testng] 00:51:01,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@39a51e9f - End of configuration. [testng] [2025-03-23 00:51:02,462] [pool-1-thread-3] Initializing /data/samples/fibre.vws: [testng] 00:51:02,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:51:02,462 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:02,463 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-03-23_00-51-02.log] [testng] 00:51:02,464 |-INFO in ch.qos.logback.core.sift.SiftProcessor@eb989b - End of configuration. [testng] [2025-03-23 00:51:03,577] [pool-1-thread-2] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 00:51:03,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:51:03,577 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:51:03,578 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-03-23_00-51-03.log] [testng] 00:51:03,578 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1298b0d1 - End of configuration. [testng] [2025-03-23 00:51:24,211] [pool-1-thread-3] Initializing /data/stephan/two sequences.vws: [testng] [2025-03-23 00:51:26,531] [pool-1-thread-12] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2025-03-23 00:51:34,993] [pool-1-thread-7] Initializing /data/imagesc-84715/working.vws: [testng] [2025-03-23 00:51:55,538] [pool-1-thread-2] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2025-03-23 00:51:59,984] [pool-1-thread-12] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-03-23 00:52:01,444] [pool-1-thread-5] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2025-03-23 00:52:11,290] [pool-1-thread-9] Initializing /data/andreas/090812E4.vws: [testng] [2025-03-23 00:52:24,145] [pool-1-thread-2] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2025-03-23 00:52:29,466] [pool-1-thread-4] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2025-03-23 00:52:33,568] [pool-1-thread-8] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2025-03-23 00:52:36,053] [pool-1-thread-6] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2025-03-23 00:52:53,109] [pool-1-thread-7] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] [2025-03-23 00:53:20,784] [pool-1-thread-3] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 51 minutes 57 seconds Finished: SUCCESS