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Started by upstream project "BIOFORMATS-test-repo" build number 61 originally caused by: Started by upstream project "Trigger" build number 68 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder [BIOFORMATS-test-folder] $ /bin/bash -xe /tmp/jenkins1447172648480280730.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_9023_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] 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] 01:24:18,466 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:24:18,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service. [testng] 01:24:18,468 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:18,470 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:24:18,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:24:18,471 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:24:18,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:24:18,472 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:18,473 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:24:18,474 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:24:18,474 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:24:18,475 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:24:18,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:24:18,752 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:24:18,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:24:18,784 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:24:18,791 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:24:18,792 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:24:18,792 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:24:18,792 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:24:18,792 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration. [testng] 01:24:18,794 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point [testng] 01:24:18,794 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 321 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-12 01:24:18,807] [main] java.version = 17.0.2 [testng] 01:24:18,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:24:18,811 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:18,860 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-12_01-24-18.log] [testng] 01:24:18,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration. [testng] [2024-05-12 01:24:18,864] [main] testng.directory = /data [testng] [2024-05-12 01:24:18,864] [main] testng.configDirectory = /config [testng] [2024-05-12 01:24:18,872] [main] testng.multiplier = 1.0 [testng] [2024-05-12 01:24:18,873] [main] testng.in-memory = false [testng] [2024-05-12 01:24:18,873] [main] testng.allow-missing = false [testng] [2024-05-12 01:24:18,873] [main] user.language = en [testng] [2024-05-12 01:24:18,874] [main] user.country = ${user.country} [testng] [2024-05-12 01:24:18,874] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-12 01:24:42,499] [main] ---------------------------------------- [testng] [2024-05-12 01:24:42,499] [main] Total files: 164 [testng] [2024-05-12 01:24:42,499] [main] Scan time: 23.625 s (144 ms/file) [testng] [2024-05-12 01:24:42,499] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-12 01:24:50,693] [pool-1-thread-1] Initializing /data/ome/Adultmidsection.lsm: [testng] 01:24:50,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:24:50,693 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,695 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-12_01-24-50.log] [testng] 01:24:50,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@35e70915 - End of configuration. [testng] [2024-05-12 01:24:50,738] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] 01:24:50,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:24:50,739 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,740 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-12_01-24-50.log] [testng] 01:24:50,740 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2c8f1cb4 - End of configuration. [testng] [2024-05-12 01:24:50,782] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne2.ppm: [testng] 01:24:50,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:24:50,783 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,784 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-12_01-24-50.log] [testng] 01:24:50,784 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5f6c0f7c - End of configuration. [testng] [2024-05-12 01:24:50,793] [pool-1-thread-10] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 01:24:50,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:24:50,794 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,795 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-12_01-24-50.log] [testng] 01:24:50,795 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7348d0a2 - End of configuration. [testng] [2024-05-12 01:24:50,832] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] 01:24:50,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:24:50,833 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,834 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-12_01-24-50.log] [testng] 01:24:50,834 |-INFO in ch.qos.logback.core.sift.SiftProcessor@665f15dd - End of configuration. [testng] [2024-05-12 01:24:50,844] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:24:50,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:24:50,844 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,845 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-12_01-24-50.log] [testng] 01:24:50,846 |-INFO in ch.qos.logback.core.sift.SiftProcessor@36a02624 - End of configuration. [testng] [2024-05-12 01:24:50,860] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 01:24:50,860 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:24:50,861 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,861 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-12_01-24-50.log] [testng] 01:24:50,862 |-INFO in ch.qos.logback.core.sift.SiftProcessor@116d3f53 - End of configuration. [testng] [2024-05-12 01:24:50,892] [pool-1-thread-6] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] 01:24:50,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:24:50,892 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,893 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-12_01-24-50.log] [testng] 01:24:50,894 |-INFO in ch.qos.logback.core.sift.SiftProcessor@45b60071 - End of configuration. [testng] [2024-05-12 01:24:50,987] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] 01:24:50,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:24:50,987 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:50,989 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-12_01-24-50.log] [testng] 01:24:50,989 |-INFO in ch.qos.logback.core.sift.SiftProcessor@19469044 - End of configuration. [testng] [2024-05-12 01:24:50,998] [pool-1-thread-4] Initializing /data/ome/tiffany.color.tiff: [testng] 01:24:50,998 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:24:50,999 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:51,000 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-12_01-24-50.log] [testng] 01:24:51,000 |-INFO in ch.qos.logback.core.sift.SiftProcessor@22ad1bf6 - End of configuration. [testng] [2024-05-12 01:24:51,046] [pool-1-thread-3] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 01:24:51,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:24:51,046 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:51,046 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-12_01-24-51.log] [testng] 01:24:51,047 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4520f0e3 - End of configuration. [testng] [2024-05-12 01:24:51,061] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:24:51,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:24:51,061 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:24:51,062 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-12_01-24-51.log] [testng] 01:24:51,062 |-INFO in ch.qos.logback.core.sift.SiftProcessor@55b002e - End of configuration. [testng] [2024-05-12 01:24:52,965] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-12 01:24:52,974] [pool-1-thread-9] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-12 01:24:52,984] [pool-1-thread-10] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-12 01:24:52,995] [pool-1-thread-1] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-05-12 01:24:53,186] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-12 01:24:53,194] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] [2024-05-12 01:24:53,577] [pool-1-thread-10] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-12 01:24:53,720] [pool-1-thread-7] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-12 01:24:53,741] [pool-1-thread-2] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] [2024-05-12 01:24:53,807] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-12 01:24:53,812] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-12 01:24:53,879] [pool-1-thread-5] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-05-12 01:24:53,907] [pool-1-thread-10] Initializing /data/ome/worm.tiff: [testng] [2024-05-12 01:24:54,010] [pool-1-thread-4] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-12 01:24:54,106] [pool-1-thread-11] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-05-12 01:24:54,155] [pool-1-thread-5] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-12 01:24:54,384] [pool-1-thread-6] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-12 01:24:54,393] [pool-1-thread-11] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-12 01:24:54,653] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] [2024-05-12 01:24:54,788] [pool-1-thread-12] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-05-12 01:24:54,822] [pool-1-thread-2] Initializing /data/ome/C1.lsm: [testng] [2024-05-12 01:24:55,143] [pool-1-thread-1] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-12 01:24:56,210] [pool-1-thread-6] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-12 01:24:56,287] [pool-1-thread-5] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-05-12 01:24:56,417] [pool-1-thread-2] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-12 01:24:57,185] [pool-1-thread-11] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-12 01:24:57,253] [pool-1-thread-4] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-05-12 01:24:57,500] [pool-1-thread-12] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-05-12 01:24:57,594] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-05-12 01:24:57,692] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-05-12 01:24:57,853] [pool-1-thread-7] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-05-12 01:24:58,086] [pool-1-thread-9] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-12 01:24:58,135] [pool-1-thread-6] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-12 01:24:58,169] [pool-1-thread-11] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-12 01:24:58,292] [pool-1-thread-8] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-12 01:24:58,349] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-12 01:24:58,416] [pool-1-thread-10] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-12 01:24:58,475] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-12 01:24:58,525] [pool-1-thread-5] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-05-12 01:24:58,586] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-12 01:24:58,724] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-12 01:24:58,776] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-05-12 01:24:58,782] [pool-1-thread-11] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-12 01:24:58,980] [pool-1-thread-9] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-12 01:24:59,033] [pool-1-thread-12] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-12 01:24:59,118] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-05-12 01:24:59,173] [pool-1-thread-11] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 2 minutes 15 seconds Finished: SUCCESS