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Started by upstream project "BIOFORMATS-test-repo" build number 258 originally caused by: Started by upstream project "Trigger" build number 282 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/jenkins7987132825665617298.sh + '[' samples = slidebook ']' ++ date +%u + '[' 7 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_40658_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] 00:34:03,850 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 00:34:03,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - No custom configurators were discovered as a service. [testng] 00:34:03,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:03,852 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 00:34:03,853 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 00:34:03,853 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 00:34:03,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 00:34:03,853 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:03,854 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 00:34:03,854 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 00:34:03,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 00:34:03,855 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 00:34:04,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 00:34:04,009 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 00:34:04,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 00:34:04,031 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 00:34:04,036 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 00:34:04,036 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 00:34:04,037 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 00:34:04,037 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 00:34:04,037 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2e3967ea - End of configuration. [testng] 00:34:04,038 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@2e6a8155 - Registering current configuration as safe fallback point [testng] 00:34:04,038 |-INFO in ch.qos.logback.classic.util.ContextInitializer@55b53d44 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 184 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-17 00:34:04,046] [main] java.version = 17.0.2 [testng] 00:34:04,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 00:34:04,049 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:34:04,088 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-17_00-34-04.log] [testng] 00:34:04,089 |-INFO in ch.qos.logback.core.sift.SiftProcessor@798162bc - End of configuration. [testng] [2024-11-17 00:34:04,091] [main] testng.directory = /data [testng] [2024-11-17 00:34:04,092] [main] testng.configDirectory = /config [testng] [2024-11-17 00:34:04,100] [main] testng.multiplier = 1.0 [testng] [2024-11-17 00:34:04,101] [main] testng.in-memory = false [testng] [2024-11-17 00:34:04,101] [main] testng.allow-missing = false [testng] [2024-11-17 00:34:04,101] [main] user.language = en [testng] [2024-11-17 00:34:04,101] [main] user.country = ${user.country} [testng] [2024-11-17 00:34:04,101] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-17 00:34:35,907] [main] ---------------------------------------- [testng] [2024-11-17 00:34:35,907] [main] Total files: 164 [testng] [2024-11-17 00:34:35,907] [main] Scan time: 31.806 s (193 ms/file) [testng] [2024-11-17 00:34:35,907] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-17 00:35:21,583] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] 00:35:21,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 00:35:21,583 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:21,585 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-17_00-35-21.log] [testng] 00:35:21,586 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2156e3f4 - End of configuration. [testng] [2024-11-17 00:35:21,995] [pool-1-thread-12] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] 00:35:21,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 00:35:21,995 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:21,996 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-17_00-35-21.log] [testng] 00:35:21,996 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25bab5d4 - End of configuration. [testng] [2024-11-17 00:35:22,256] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] 00:35:22,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 00:35:22,257 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:22,257 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-17_00-35-22.log] [testng] 00:35:22,258 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e679d57 - End of configuration. [testng] [2024-11-17 00:35:22,536] [pool-1-thread-10] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 00:35:22,536 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 00:35:22,537 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:22,538 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-17_00-35-22.log] [testng] 00:35:22,538 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6c2eaf4 - End of configuration. [testng] [2024-11-17 00:35:22,654] [pool-1-thread-9] Initializing /data/openjpeg/thumb_facade.jpg: [testng] 00:35:22,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 00:35:22,654 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:22,655 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-17_00-35-22.log] [testng] 00:35:22,655 |-INFO in ch.qos.logback.core.sift.SiftProcessor@49954ad0 - End of configuration. [testng] [2024-11-17 00:35:22,697] [pool-1-thread-8] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] 00:35:22,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 00:35:22,697 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:22,698 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-17_00-35-22.log] [testng] 00:35:22,698 |-INFO in ch.qos.logback.core.sift.SiftProcessor@32a428f3 - End of configuration. [testng] [2024-11-17 00:35:22,743] [pool-1-thread-7] Initializing /data/openjpeg/Cevennes2.jp2: [testng] 00:35:22,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 00:35:22,743 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:22,744 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-17_00-35-22.log] [testng] 00:35:22,744 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f24812e - End of configuration. [testng] [2024-11-17 00:35:22,955] [pool-1-thread-6] Initializing /data/ome/embryo.lsm: [testng] 00:35:22,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 00:35:22,955 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:22,956 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-17_00-35-22.log] [testng] 00:35:22,956 |-INFO in ch.qos.logback.core.sift.SiftProcessor@56ee7015 - End of configuration. [testng] [2024-11-17 00:35:23,285] [pool-1-thread-5] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] 00:35:23,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 00:35:23,285 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:23,286 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-17_00-35-23.log] [testng] 00:35:23,286 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6732c8bc - End of configuration. [testng] [2024-11-17 00:35:23,578] [pool-1-thread-4] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] 00:35:23,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 00:35:23,578 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:23,579 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-17_00-35-23.log] [testng] 00:35:23,579 |-INFO in ch.qos.logback.core.sift.SiftProcessor@76063626 - End of configuration. [testng] [2024-11-17 00:35:23,716] [pool-1-thread-3] Initializing /data/ome/tiffany.color.tiff: [testng] 00:35:23,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 00:35:23,716 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:23,717 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-17_00-35-23.log] [testng] 00:35:23,717 |-INFO in ch.qos.logback.core.sift.SiftProcessor@af8b938 - End of configuration. [testng] [2024-11-17 00:35:25,082] [pool-1-thread-2] Initializing /data/ome/anusgfpzs.lsm: [testng] 00:35:25,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 00:35:25,082 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 00:35:25,083 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-17_00-35-25.log] [testng] 00:35:25,083 |-INFO in ch.qos.logback.core.sift.SiftProcessor@7b2ebded - End of configuration. [testng] [2024-11-17 00:35:28,734] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-11-17 00:35:28,877] [pool-1-thread-10] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-11-17 00:35:29,153] [pool-1-thread-9] Initializing /data/ome/compressed2ChZ.lsm: [testng] [2024-11-17 00:35:29,798] [pool-1-thread-8] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-11-17 00:35:30,835] [pool-1-thread-7] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-11-17 00:35:31,760] [pool-1-thread-12] Initializing /data/openjpeg/Facade.pnm: [testng] [2024-11-17 00:35:31,943] [pool-1-thread-2] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-11-17 00:35:32,765] [pool-1-thread-6] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-11-17 00:35:34,059] [pool-1-thread-5] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-11-17 00:35:34,181] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes2.bmp: [testng] [2024-11-17 00:35:34,333] [pool-1-thread-10] Initializing /data/openjpeg/Rome.jp2: [testng] [2024-11-17 00:35:35,183] [pool-1-thread-4] Initializing /data/ome/cb_1.r3d: [testng] [2024-11-17 00:35:35,868] [pool-1-thread-8] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-11-17 00:35:36,667] [pool-1-thread-3] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-11-17 00:35:37,135] [pool-1-thread-1] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-11-17 00:35:38,200] [pool-1-thread-9] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-11-17 00:35:38,469] [pool-1-thread-11] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] [2024-11-17 00:35:38,578] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] [2024-11-17 00:35:39,469] [pool-1-thread-4] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-11-17 00:35:39,813] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-11-17 00:35:39,871] [pool-1-thread-6] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-11-17 00:35:40,154] [pool-1-thread-2] Initializing /data/ome/C1.lsm: [testng] [2024-11-17 00:35:40,584] [pool-1-thread-5] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-11-17 00:35:42,188] [pool-1-thread-12] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-11-17 00:35:43,164] [pool-1-thread-11] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-11-17 00:35:43,608] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-11-17 00:35:43,872] [pool-1-thread-8] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-11-17 00:35:44,020] [pool-1-thread-9] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-11-17 00:35:44,195] [pool-1-thread-10] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-11-17 00:35:46,353] [pool-1-thread-8] Initializing /data/ome/654Atemp.stk: [testng] [2024-11-17 00:35:48,100] [pool-1-thread-7] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-11-17 00:36:14,309] [pool-1-thread-4] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-11-17 00:36:14,875] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-11-17 00:36:14,981] [pool-1-thread-6] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-11-17 00:36:15,390] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-11-17 00:36:17,897] [pool-1-thread-9] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] [2024-11-17 00:36:18,783] [pool-1-thread-12] Initializing /data/openjpeg/Bretagne1.j2k: [testng] [2024-11-17 00:36:20,002] [pool-1-thread-2] Initializing /data/10-31 E1/10-31 E1.tif: [testng] [2024-11-17 00:36:21,709] [pool-1-thread-4] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-11-17 00:36:22,784] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne1.ppm: [testng] [2024-11-17 00:36:24,395] [pool-1-thread-9] Initializing /data/sdub/sdub.pattern: [testng] [2024-11-17 00:36:31,776] [pool-1-thread-10] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-11-17 00:36:32,053] [pool-1-thread-12] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-11-17 00:36:33,584] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-11-17 00:36:34,081] [pool-1-thread-11] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-11-17 00:36:34,229] [pool-1-thread-3] Initializing /data/openjpeg/Bretagne2.j2k: [testng] [2024-11-17 00:36:34,851] [pool-1-thread-12] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 3127, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 4 minutes 16 seconds Finished: SUCCESS