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Started by upstream project "BIOFORMATS-test-repo" build number 344 originally caused by: Started by upstream project "Trigger" build number 370 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@8 [BIOFORMATS-test-folder@8] $ /bin/bash -xe /tmp/jenkins1608574770033112099.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_54737_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:25:56,678 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.15 [testng] 01:25:56,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - No custom configurators were discovered as a service. [testng] 01:25:56,679 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:56,681 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:25:56,681 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:25:56,682 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:25:56,682 |-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] 01:25:56,682 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:56,683 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:25:56,683 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:25:56,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:25:56,684 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:25:56,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:25:56,846 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:25:56,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:25:56,872 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:25:56,879 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:25:56,879 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:25:56,879 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:25:56,880 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:25:56,880 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@4310d43 - End of configuration. [testng] 01:25:56,881 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@1b11171f - Registering current configuration as safe fallback point [testng] 01:25:56,881 |-INFO in ch.qos.logback.classic.util.ContextInitializer@36d585c - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 198 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2025-02-13 01:25:56,890] [main] java.version = 21 [testng] 01:25:56,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:25:56,894 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:25:56,939 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2025-02-13_01-25-56.log] [testng] 01:25:56,940 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69504ae9 - End of configuration. [testng] [2025-02-13 01:25:56,943] [main] testng.directory = /data [testng] [2025-02-13 01:25:56,943] [main] testng.configDirectory = /config [testng] [2025-02-13 01:25:56,953] [main] testng.multiplier = 1.0 [testng] [2025-02-13 01:25:56,953] [main] testng.in-memory = false [testng] [2025-02-13 01:25:56,953] [main] testng.allow-missing = false [testng] [2025-02-13 01:25:56,954] [main] user.language = en [testng] [2025-02-13 01:25:56,954] [main] user.country = ${user.country} [testng] [2025-02-13 01:25:56,954] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2025-02-13 01:26:14,395] [main] ---------------------------------------- [testng] [2025-02-13 01:26:14,395] [main] Total files: 46 [testng] [2025-02-13 01:26:14,395] [main] Scan time: 17.441 s (379 ms/file) [testng] [2025-02-13 01:26:14,395] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2025-02-13 01:27:10,642] [pool-1-thread-1] Initializing /data/christian/080807epi/080807epi2.vws: [testng] 01:27:10,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:27:10,643 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:10,645 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2025-02-13_01-27-10.log] [testng] 01:27:10,645 |-INFO in ch.qos.logback.core.sift.SiftProcessor@57e3d7ef - End of configuration. [testng] [2025-02-13 01:27:11,232] [pool-1-thread-12] Initializing /data/samples/fibre.vws: [testng] 01:27:11,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:27:11,232 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:11,233 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2025-02-13_01-27-11.log] [testng] 01:27:11,234 |-INFO in ch.qos.logback.core.sift.SiftProcessor@595f955 - End of configuration. [testng] [2025-02-13 01:27:11,590] [pool-1-thread-11] Initializing /data/andreas/090812E4.vws: [testng] 01:27:11,590 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:27:11,591 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:11,592 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2025-02-13_01-27-11.log] [testng] 01:27:11,593 |-INFO in ch.qos.logback.core.sift.SiftProcessor@374ac1c7 - End of configuration. [testng] [2025-02-13 01:27:13,686] [pool-1-thread-10] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] 01:27:13,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:27:13,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:13,687 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2025-02-13_01-27-13.log] [testng] 01:27:13,688 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22d2571f - End of configuration. [testng] [2025-02-13 01:27:15,642] [pool-1-thread-9] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] 01:27:15,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:27:15,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:15,643 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2025-02-13_01-27-15.log] [testng] 01:27:15,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c47c972 - End of configuration. [testng] [2025-02-13 01:27:17,070] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 01:27:17,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:27:17,070 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:17,071 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2025-02-13_01-27-17.log] [testng] 01:27:17,071 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63183898 - End of configuration. [testng] [2025-02-13 01:27:17,541] [pool-1-thread-7] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 01:27:17,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:27:17,542 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:17,542 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2025-02-13_01-27-17.log] [testng] 01:27:17,543 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f394089 - End of configuration. [testng] [2025-02-13 01:27:18,205] [pool-1-thread-6] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 01:27:18,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:27:18,205 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:18,205 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2025-02-13_01-27-18.log] [testng] 01:27:18,206 |-INFO in ch.qos.logback.core.sift.SiftProcessor@431ce2ed - End of configuration. [testng] [2025-02-13 01:27:19,598] [pool-1-thread-5] Initializing /data/stephan/two sequences.vws: [testng] 01:27:19,598 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:27:19,599 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:19,599 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2025-02-13_01-27-19.log] [testng] 01:27:19,599 |-INFO in ch.qos.logback.core.sift.SiftProcessor@735b60d1 - End of configuration. [testng] [2025-02-13 01:27:20,163] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] 01:27:20,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:27:20,163 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:20,163 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2025-02-13_01-27-20.log] [testng] 01:27:20,164 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47bfbaa8 - End of configuration. [testng] [2025-02-13 01:27:21,063] [pool-1-thread-3] Initializing /data/andreas/090811E1.vws: [testng] 01:27:21,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:27:21,063 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:21,064 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2025-02-13_01-27-21.log] [testng] 01:27:21,064 |-INFO in ch.qos.logback.core.sift.SiftProcessor@362a0c31 - End of configuration. [testng] [2025-02-13 01:27:26,617] [pool-1-thread-2] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 01:27:26,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:27:26,617 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:27:26,617 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2025-02-13_01-27-26.log] [testng] 01:27:26,618 |-INFO in ch.qos.logback.core.sift.SiftProcessor@59198ba9 - End of configuration. [testng] [2025-02-13 01:27:37,399] [pool-1-thread-12] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] [2025-02-13 01:27:40,064] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] [2025-02-13 01:27:41,994] [pool-1-thread-9] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2025-02-13 01:27:51,163] [pool-1-thread-1] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] [2025-02-13 01:27:52,069] [pool-1-thread-9] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2025-02-13 01:27:52,830] [pool-1-thread-6] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2025-02-13 01:28:00,107] [pool-1-thread-8] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2025-02-13 01:28:02,831] [pool-1-thread-7] Initializing /data/imagesc-84715/not working.vws: [testng] [2025-02-13 01:28:04,910] [pool-1-thread-4] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] [2025-02-13 01:28:11,543] [pool-1-thread-12] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2025-02-13 01:28:14,112] [pool-1-thread-5] Initializing /data/gerhard/test.vws: [testng] [2025-02-13 01:28:21,716] [pool-1-thread-5] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] [2025-02-13 01:28:28,253] [pool-1-thread-7] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1325, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 17 minutes 11 seconds Finished: SUCCESS