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Started by upstream project "BIOFORMATS-test-repo" build number 225 originally caused by: Started by user devspace 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/jenkins11939730117117301182.sh + '[' tillvision = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35505_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 15:17:57,807 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 15:17:57,808 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 15:17:57,808 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:17:57,809 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 15:17:57,810 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 15:17:57,810 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 15:17:57,810 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 15:17:57,810 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:17:57,811 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 15:17:57,811 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 15:17:57,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 15:17:57,812 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 15:17:57,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 15:17:57,959 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 15:17:57,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 15:17:57,982 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 15:17:57,987 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 15:17:57,988 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 15:17:57,988 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 15:17:57,988 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 15:17:57,988 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 15:17:57,989 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 15:17:57,989 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 178 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 15:17:57,997] [main] java.version = 21 [testng] 15:17:58,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 15:17:58,000 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:17:58,039 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_15-17-58.log] [testng] 15:17:58,041 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 15:17:58,042] [main] testng.directory = /data [testng] [2024-10-17 15:17:58,042] [main] testng.configDirectory = /config [testng] [2024-10-17 15:17:58,050] [main] testng.multiplier = 1.0 [testng] [2024-10-17 15:17:58,051] [main] testng.in-memory = false [testng] [2024-10-17 15:17:58,051] [main] testng.allow-missing = false [testng] [2024-10-17 15:17:58,051] [main] user.language = en [testng] [2024-10-17 15:17:58,051] [main] user.country = ${user.country} [testng] [2024-10-17 15:17:58,051] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 15:19:27,328] [main] ---------------------------------------- [testng] [2024-10-17 15:19:27,328] [main] Total files: 46 [testng] [2024-10-17 15:19:27,328] [main] Scan time: 89.277 s (1940 ms/file) [testng] [2024-10-17 15:19:27,329] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 25 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 15:22:42,082] [pool-1-thread-1] Initializing /data/qinghai/TillvisIOn Sample Dataset/Bgr.vws: [testng] 15:22:42,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 15:22:42,083 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:22:42,084 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-10-17_15-22-42.log] [testng] 15:22:42,084 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4417a47 - End of configuration. [testng] [2024-10-17 15:22:45,215] [pool-1-thread-12] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated BAM_Wrkspc1.vws: [testng] 15:22:45,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 15:22:45,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:22:45,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-10-17_15-22-45.log] [testng] 15:22:45,216 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f6dd29d - End of configuration. [testng] [2024-10-17 15:22:48,782] [pool-1-thread-11] Initializing /data/christian/080807ionophore/080807ionophore3.vws: [testng] 15:22:48,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 15:22:48,782 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:22:48,783 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-10-17_15-22-48.log] [testng] 15:22:48,783 |-INFO in ch.qos.logback.core.sift.SiftProcessor@672d68b3 - End of configuration. [testng] [2024-10-17 15:22:52,286] [pool-1-thread-10] Initializing /data/gerhard/test.vws: [testng] 15:22:52,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 15:22:52,286 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:22:52,287 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-10-17_15-22-52.log] [testng] 15:22:52,287 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53da0100 - End of configuration. [testng] [2024-10-17 15:22:53,796] [pool-1-thread-9] Initializing /data/imagesc-84715/not working.vws: [testng] 15:22:53,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 15:22:53,796 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:22:53,797 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-10-17_15-22-53.log] [testng] 15:22:53,797 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22d2571f - End of configuration. [testng] [2024-10-17 15:22:56,249] [pool-1-thread-8] Initializing /data/venu/060310/Visible parts of Fluorescence 380nm1_test1.tif: [testng] 15:22:56,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 15:22:56,249 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:22:56,250 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-10-17_15-22-56.log] [testng] 15:22:56,250 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5c47c972 - End of configuration. [testng] [2024-10-17 15:23:06,163] [pool-1-thread-7] Initializing /data/venu/060310/drug addition protocol testing_Wrkspc3.vws: [testng] 15:23:06,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 15:23:06,164 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:23:06,164 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-10-17_15-23-06.log] [testng] 15:23:06,165 |-INFO in ch.qos.logback.core.sift.SiftProcessor@63183898 - End of configuration. [testng] [2024-10-17 15:23:10,105] [pool-1-thread-6] Initializing /data/venu/060310/1_glass bottom dish_fluorescence snapshot.tif: [testng] 15:23:10,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 15:23:10,105 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:23:10,105 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-10-17_15-23-10.log] [testng] 15:23:10,106 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f394089 - End of configuration. [testng] [2024-10-17 15:23:20,088] [pool-1-thread-5] Initializing /data/ian/working_tillvision_vws/20120322.vws: [testng] 15:23:20,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 15:23:20,088 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:23:20,089 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-10-17_15-23-20.log] [testng] 15:23:20,089 |-INFO in ch.qos.logback.core.sift.SiftProcessor@431ce2ed - End of configuration. [testng] [2024-10-17 15:23:28,453] [pool-1-thread-4] Initializing /data/imagesc-84715/working.vws: [testng] 15:23:28,453 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 15:23:28,454 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:23:28,455 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-10-17_15-23-28.log] [testng] 15:23:28,455 |-INFO in ch.qos.logback.core.sift.SiftProcessor@735b60d1 - End of configuration. [testng] [2024-10-17 15:23:32,228] [pool-1-thread-3] Initializing /data/venu/060310/1_ drug addition actual test_ glass_Wrkspc6.vws: [testng] 15:23:32,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 15:23:32,228 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:23:32,229 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-10-17_15-23-32.log] [testng] 15:23:32,229 |-INFO in ch.qos.logback.core.sift.SiftProcessor@47bfbaa8 - End of configuration. [testng] [2024-10-17 15:23:34,641] [pool-1-thread-2] Initializing /data/andreas/090812E4.vws: [testng] 15:23:34,641 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 15:23:34,642 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 15:23:34,642 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-10-17_15-23-34.log] [testng] 15:23:34,643 |-INFO in ch.qos.logback.core.sift.SiftProcessor@362a0c31 - End of configuration. [testng] [2024-10-17 15:24:22,235] [pool-1-thread-10] Initializing /data/oliver/TillVision-Data-2-from-Oliver-Mueller-Homburg-Germany/2006 DG2 V1 Indo-1 Ratte.vws: [testng] [2024-10-17 15:24:43,017] [pool-1-thread-6] Initializing /data/venu/060310/drug addition _BAM.vws: [testng] [2024-10-17 15:24:46,683] [pool-1-thread-8] Initializing /data/christian/080807epi/080807epi2.vws: [testng] [2024-10-17 15:25:40,016] [pool-1-thread-11] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc1.vws: [testng] [2024-10-17 15:26:02,410] [pool-1-thread-9] Initializing /data/venu/061410/Rat LD muscle fibers Wrkspc3.vws: [testng] [2024-10-17 15:26:17,548] [pool-1-thread-8] Initializing /data/venu/061410/Differentiating MPCs on Matrigel coated glass_Wrkspc2.vws: [testng] [2024-10-17 15:26:30,967] [pool-1-thread-3] Initializing /data/andreas/090811E1.vws: [testng] [2024-10-17 15:26:56,510] [pool-1-thread-12] Initializing /data/venu/060310/1_glass bottom dish snapshot.tif: [testng] [2024-10-17 15:27:08,208] [pool-1-thread-1] Initializing /data/venu/060310/060310_glass_Wrkspc1.vws: [testng] [2024-10-17 15:27:12,856] [pool-1-thread-4] Initializing /data/stephan/two sequences.vws: [testng] [2024-10-17 15:27:28,018] [pool-1-thread-7] Initializing /data/samples/fibre.vws: [testng] [2024-10-17 15:27:36,788] [pool-1-thread-6] Initializing /data/venu/060310/Fluorescence 340nm1_test 1.tif: [testng] [2024-10-17 15:27:47,917] [pool-1-thread-12] Initializing /data/ian/non_working_tillvision_vws/20120404.vws: [testng] 16:47:02,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 16:47:02,687 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 16:47:02,688 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_16-47-02.log] [testng] 16:47:02,689 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4d8286c4 - 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: 89 minutes 7 seconds Finished: SUCCESS