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Started by upstream project "BIOFORMATS-test-repo" build number 223 originally caused by: Started by upstream project "Trigger" build number 250 originally caused by: Started by timer 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/jenkins3733195657002497582.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_35363_merge_ci -v /uod/idr/repos/curated/samples:/data -v /uod/idr-scratch/merge-ci/curated/samples:/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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 02:10:22,378 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 02:10:22,379 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - No custom configurators were discovered as a service. [testng] 02:10:22,379 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:22,380 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 02:10:22,380 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 02:10:22,381 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 02:10:22,381 |-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] 02:10:22,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:22,381 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 02:10:22,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 02:10:22,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 02:10:22,382 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 02:10:22,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 02:10:22,535 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 02:10:22,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 02:10:22,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 02:10:22,570 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 02:10:22,570 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 02:10:22,570 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 02:10:22,571 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 02:10:22,571 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@29215f06 - End of configuration. [testng] 02:10:22,572 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@b9b00e0 - Registering current configuration as safe fallback point [testng] 02:10:22,572 |-INFO in ch.qos.logback.classic.util.ContextInitializer@4f67eb2a - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 191 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-10-17 02:10:22,580] [main] java.version = 21 [testng] 02:10:22,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 02:10:22,584 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:10:22,623 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-10-17_02-10-22.log] [testng] 02:10:22,624 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-10-17 02:10:22,626] [main] testng.directory = /data [testng] [2024-10-17 02:10:22,626] [main] testng.configDirectory = /config [testng] [2024-10-17 02:10:22,634] [main] testng.multiplier = 1.0 [testng] [2024-10-17 02:10:22,634] [main] testng.in-memory = false [testng] [2024-10-17 02:10:22,635] [main] testng.allow-missing = false [testng] [2024-10-17 02:10:22,635] [main] user.language = en [testng] [2024-10-17 02:10:22,635] [main] user.country = ${user.country} [testng] [2024-10-17 02:10:22,635] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-10-17 02:15:05,785] [main] ---------------------------------------- [testng] [2024-10-17 02:15:05,786] [main] Total files: 164 [testng] [2024-10-17 02:15:05,786] [main] Scan time: 283.15 s (1726 ms/file) [testng] [2024-10-17 02:15:05,786] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-10-17 02:24:03,825] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 02:24:03,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 02:24:03,826 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:03,827 |-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_02-24-03.log] [testng] 02:24:03,828 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2995a955 - End of configuration. [testng] [2024-10-17 02:24:10,285] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] 02:24:10,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 02:24:10,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:10,286 |-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_02-24-10.log] [testng] 02:24:10,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@11587fd1 - End of configuration. [testng] [2024-10-17 02:24:11,808] [pool-1-thread-11] Initializing /data/ome/C1.lsm: [testng] 02:24:11,809 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 02:24:11,809 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:11,810 |-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_02-24-11.log] [testng] 02:24:11,810 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b1a2b47 - End of configuration. [testng] [2024-10-17 02:24:18,230] [pool-1-thread-10] Initializing /data/openjpeg/Facade.bmp: [testng] 02:24:18,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 02:24:18,230 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:18,230 |-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_02-24-18.log] [testng] 02:24:18,231 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e071050 - End of configuration. [testng] [2024-10-17 02:24:19,238] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 02:24:19,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 02:24:19,238 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:19,239 |-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_02-24-19.log] [testng] 02:24:19,239 |-INFO in ch.qos.logback.core.sift.SiftProcessor@62c7e220 - End of configuration. [testng] [2024-10-17 02:24:20,800] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 02:24:20,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 02:24:20,800 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:20,801 |-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_02-24-20.log] [testng] 02:24:20,801 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6b355ef7 - End of configuration. [testng] [2024-10-17 02:24:22,595] [pool-1-thread-7] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] 02:24:22,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 02:24:22,595 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:22,596 |-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_02-24-22.log] [testng] 02:24:22,596 |-INFO in ch.qos.logback.core.sift.SiftProcessor@75b9aa2b - End of configuration. [testng] [2024-10-17 02:24:37,461] [pool-1-thread-6] Initializing /data/openjpeg/Rome.jp2: [testng] 02:24:37,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 02:24:37,461 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:37,462 |-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_02-24-37.log] [testng] 02:24:37,463 |-INFO in ch.qos.logback.core.sift.SiftProcessor@61a35e4d - End of configuration. [testng] [2024-10-17 02:24:41,658] [pool-1-thread-5] Initializing /data/ome/CHOBI_d3d.dv: [testng] 02:24:41,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 02:24:41,658 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:41,659 |-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_02-24-41.log] [testng] 02:24:41,659 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7e284641 - End of configuration. [testng] [2024-10-17 02:24:43,616] [pool-1-thread-4] Initializing /data/ome/011B1_Morph.HTD: [testng] 02:24:43,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 02:24:43,616 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:43,617 |-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_02-24-43.log] [testng] 02:24:43,617 |-INFO in ch.qos.logback.core.sift.SiftProcessor@78d8f40d - End of configuration. [testng] [2024-10-17 02:24:51,756] [pool-1-thread-3] Initializing /data/ome/654Atemp.stk: [testng] 02:24:51,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 02:24:51,756 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:24:51,757 |-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_02-24-51.log] [testng] 02:24:51,757 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76f12e3b - End of configuration. [testng] [2024-10-17 02:25:05,563] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] 02:25:05,563 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 02:25:05,564 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 02:25:05,564 |-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_02-25-05.log] [testng] 02:25:05,564 |-INFO in ch.qos.logback.core.sift.SiftProcessor@edfd017 - End of configuration. [testng] [2024-10-17 02:25:22,034] [pool-1-thread-9] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-10-17 02:25:23,682] [pool-1-thread-12] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-10-17 02:25:30,653] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-10-17 02:25:33,660] [pool-1-thread-5] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-10-17 02:25:46,567] [pool-1-thread-9] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-10-17 02:25:53,725] [pool-1-thread-8] Initializing /data/sdub/sdub.pattern: [testng] [2024-10-17 02:27:00,665] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-10-17 02:27:05,453] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-10-17 02:27:12,374] [pool-1-thread-6] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-10-17 02:27:13,732] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-10-17 02:27:18,741] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-10-17 02:27:27,679] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-10-17 02:27:29,251] [pool-1-thread-6] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-10-17 02:27:30,615] [pool-1-thread-12] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-10-17 02:27:41,234] [pool-1-thread-2] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-10-17 02:31:54,506] [pool-1-thread-11] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-10-17 02:32:08,293] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-10-17 02:32:16,579] [pool-1-thread-9] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-10-17 02:32:21,272] [pool-1-thread-5] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-10-17 02:32:26,390] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-10-17 02:32:31,676] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-10-17 02:32:35,436] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-10-17 02:32:46,207] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-10-17 02:32:56,225] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-10-17 02:33:00,857] [pool-1-thread-1] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-10-17 02:33:06,681] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-10-17 02:33:18,090] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-10-17 02:33:23,885] [pool-1-thread-7] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-10-17 02:33:29,587] [pool-1-thread-5] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-10-17 02:33:35,289] [pool-1-thread-10] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-10-17 02:33:40,989] [pool-1-thread-3] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-10-17 02:33:43,530] [pool-1-thread-11] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-10-17 02:33:58,584] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-10-17 02:34:03,128] [pool-1-thread-4] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-10-17 02:34:04,370] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-10-17 02:34:11,476] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-10-17 02:34:17,896] [pool-1-thread-6] Initializing /data/ome/worm.tiff: [testng] [2024-10-17 02:34:31,090] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-10-17 02:34:32,023] [pool-1-thread-10] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-10-17 02:34:33,145] [pool-1-thread-5] Initializing /data/ome/cb_1.r3d: [testng] [2024-10-17 02:34:39,969] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-10-17 02:34:47,671] [pool-1-thread-4] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-10-17 02:34:53,818] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-10-17 02:34:54,946] [pool-1-thread-7] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-10-17 02:34:59,255] [pool-1-thread-10] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-10-17 02:35:04,546] [pool-1-thread-5] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-10-17 02:35:11,035] [pool-1-thread-1] Initializing /data/ome/tiffany.color.tiff: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 42 minutes 44 seconds Finished: SUCCESS