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Started by upstream project "BIOFORMATS-test-repo" build number 288 originally caused by: Started by upstream project "Trigger" build number 307 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@10 [BIOFORMATS-test-folder@10] $ /bin/bash -xe /tmp/jenkins9867649382327581231.sh + '[' bruker = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_45556_merge_ci -v /uod/idr/repos/curated/bruker:/data -v /uod/idr-scratch/merge-ci/curated/bruker:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 08:25:05,581 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 08:25:05,582 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 08:25:05,582 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:25:05,583 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 08:25:05,583 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 08:25:05,583 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 08:25:05,584 |-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] 08:25:05,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:25:05,584 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 08:25:05,585 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 08:25:05,585 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 08:25:05,585 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 08:25:05,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 08:25:05,731 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 08:25:05,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 08:25:05,754 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 08:25:05,760 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 08:25:05,760 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 08:25:05,760 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 08:25:05,760 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 08:25:05,760 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 08:25:05,761 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 08:25:05,761 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 177 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-12-12 08:25:05,769] [main] java.version = 21 [testng] 08:25:05,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 08:25:05,772 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 08:25:05,811 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-12-12_08-25-05.log] [testng] 08:25:05,812 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-12-12 08:25:05,814] [main] testng.directory = /data [testng] [2024-12-12 08:25:05,814] [main] testng.configDirectory = /config [testng] [2024-12-12 08:25:05,822] [main] testng.multiplier = 1.0 [testng] [2024-12-12 08:25:05,822] [main] testng.in-memory = false [testng] [2024-12-12 08:25:05,822] [main] testng.allow-missing = false [testng] [2024-12-12 08:25:05,822] [main] user.language = en [testng] [2024-12-12 08:25:05,823] [main] user.country = ${user.country} [testng] [2024-12-12 08:25:05,823] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-12-12 10:03:13,128] [main] ---------------------------------------- [testng] [2024-12-12 10:03:13,128] [main] Total files: 826 [testng] [2024-12-12 10:03:13,128] [main] Scan time: 5887.305 s (7127 ms/file) [testng] [2024-12-12 10:03:13,129] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 17 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-12-12 10:11:58,092] [pool-1-thread-1] Initializing /data/wis/tiffs/RAf_100110_091_Scan7_Slice9_TR6.tif: [testng] 10:11:58,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 10:11:58,093 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:11:58,094 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-12-12_10-11-58.log] [testng] 10:11:58,094 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7aba8d24 - End of configuration. [testng] [2024-12-12 10:12:03,132] [pool-1-thread-12] Initializing /data/wis/RA_060110.051/1/acqp: [testng] 10:12:03,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 10:12:03,132 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:03,133 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-12-12_10-12-03.log] [testng] 10:12:03,133 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2653f72b - End of configuration. [testng] [2024-12-12 10:12:15,772] [pool-1-thread-11] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice3.tif: [testng] 10:12:15,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 10:12:15,773 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:15,773 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-12-12_10-12-15.log] [testng] 10:12:15,774 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3dbd6625 - End of configuration. [testng] [2024-12-12 10:12:21,530] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan2_slice1.tif: [testng] 10:12:21,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 10:12:21,530 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:21,531 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-12-12_10-12-21.log] [testng] 10:12:21,531 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6ed2469 - End of configuration. [testng] [2024-12-12 10:12:26,885] [pool-1-thread-9] Initializing /data/wis/RA_240912_m1.g71/1/acqp: [testng] 10:12:26,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 10:12:26,885 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:26,886 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-12-12_10-12-26.log] [testng] 10:12:26,886 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e519c94 - End of configuration. [testng] [2024-12-12 10:12:43,690] [pool-1-thread-8] Initializing /data/wis/tiffs/RAf_100110_091_Scan3_Slice5.tif: [testng] 10:12:43,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 10:12:43,690 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:43,691 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-12-12_10-12-43.log] [testng] 10:12:43,691 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1ee1bb3d - End of configuration. [testng] [2024-12-12 10:12:48,874] [pool-1-thread-7] Initializing /data/wis/tiffs/RA_060110_051_scan6_slice5.tif: [testng] 10:12:48,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 10:12:48,874 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:48,874 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-12-12_10-12-48.log] [testng] 10:12:48,875 |-INFO in ch.qos.logback.core.sift.SiftProcessor@500fb382 - End of configuration. [testng] [2024-12-12 10:12:53,930] [pool-1-thread-6] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo6.tif: [testng] 10:12:53,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 10:12:53,931 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:53,931 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-12-12_10-12-53.log] [testng] 10:12:53,932 |-INFO in ch.qos.logback.core.sift.SiftProcessor@919ca1a - End of configuration. [testng] [2024-12-12 10:12:58,849] [pool-1-thread-5] Initializing /data/wis/tiffs/RA_060110_051_scan2_slice6.tif: [testng] 10:12:58,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 10:12:58,849 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:12:58,849 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-12-12_10-12-58.log] [testng] 10:12:58,850 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19e04b61 - End of configuration. [testng] [2024-12-12 10:13:03,786] [pool-1-thread-4] Initializing /data/wis/tiffs/hd111104p3_sH3_scan1_slice1.tif: [testng] 10:13:03,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 10:13:03,786 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:13:03,787 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-12-12_10-13-03.log] [testng] 10:13:03,787 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6e741ca5 - End of configuration. [testng] [2024-12-12 10:13:08,744] [pool-1-thread-3] Initializing /data/wis/tiffs/RAf_100110_091_Scan6_Slice5_echo1.tif: [testng] 10:13:08,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 10:13:08,744 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:13:08,745 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-12-12_10-13-08.log] [testng] 10:13:08,745 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6a7b5593 - End of configuration. [testng] [2024-12-12 10:13:13,727] [pool-1-thread-2] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice1.tif: [testng] 10:13:13,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 10:13:13,727 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 10:13:13,728 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-12-12_10-13-13.log] [testng] 10:13:13,728 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7c28bd54 - End of configuration. [testng] [2024-12-12 10:13:48,881] [pool-1-thread-5] Initializing /data/wis/tiffs/RAf_100110_091_Scan8_Slice9_diff15.tif: [testng] [2024-12-12 10:13:54,528] [pool-1-thread-11] Initializing /data/wis/tiffs/RA_060110_051_scan1_slice3.tif: [testng] [2024-12-12 10:14:00,295] [pool-1-thread-10] Initializing /data/wis/tiffs/hd111104p3_sH3_scan5_slice1.tif: [testng] [2024-12-12 10:14:06,079] [pool-1-thread-8] Initializing /data/samples/dimension-mismatch/1/acqp: [testng] [2024-12-12 10:14:12,861] [pool-1-thread-7] Initializing /data/wis/tiffs/hd111104p3_sH3_scan3_slice1_echo1.tif: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 901, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 163 minutes 24 seconds Finished: SUCCESS