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Started by upstream project "BIOFORMATS-test-repo" build number 72 originally caused by: Started by upstream project "Trigger" build number 80 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@5 [BIOFORMATS-test-folder@5] $ /bin/bash -xe /tmp/jenkins12855310344833052746.sh + '[' samples = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_10827_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warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options.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] 01:23:18,822 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14 [testng] 01:23:18,824 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - No custom configurators were discovered as a service. [testng] 01:23:18,824 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:18,826 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator [testng] 01:23:18,827 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo] [testng] 01:23:18,828 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo] [testng] 01:23:18,828 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 2 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY [testng] 01:23:18,828 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:18,829 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator [testng] 01:23:18,830 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}] [testng] 01:23:18,830 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml] [testng] 01:23:18,830 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml] [testng] 01:23:19,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:23:19,045 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:23:19,079 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:23:19,080 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:23:19,087 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:23:19,087 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:23:19,087 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:23:19,088 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:23:19,088 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@d9345cd - End of configuration. [testng] 01:23:19,089 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@48aca48b - Registering current configuration as safe fallback point [testng] 01:23:19,089 |-INFO in ch.qos.logback.classic.util.ContextInitializer@46fa7c39 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 260 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-05-23 01:23:19,100] [main] java.version = 21 [testng] 01:23:19,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:23:19,104 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:19,154 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-23_01-23-19.log] [testng] 01:23:19,156 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71687585 - End of configuration. [testng] [2024-05-23 01:23:19,159] [main] testng.directory = /data [testng] [2024-05-23 01:23:19,159] [main] testng.configDirectory = /config [testng] [2024-05-23 01:23:19,173] [main] testng.multiplier = 1.0 [testng] [2024-05-23 01:23:19,174] [main] testng.in-memory = false [testng] [2024-05-23 01:23:19,175] [main] testng.allow-missing = false [testng] [2024-05-23 01:23:19,175] [main] user.language = en [testng] [2024-05-23 01:23:19,175] [main] user.country = ${user.country} [testng] [2024-05-23 01:23:19,175] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-05-23 01:23:38,933] [main] ---------------------------------------- [testng] [2024-05-23 01:23:38,933] [main] Total files: 164 [testng] [2024-05-23 01:23:38,933] [main] Scan time: 19.758 s (120 ms/file) [testng] [2024-05-23 01:23:38,934] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 59 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-05-23 01:23:48,430] [pool-1-thread-1] Initializing /data/openjpeg/thumb_FacadeCOMP.jpg: [testng] 01:23:48,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:23:48,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,433 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-23_01-23-48.log] [testng] 01:23:48,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@69b1a865 - End of configuration. [testng] [2024-05-23 01:23:48,448] [pool-1-thread-12] Initializing /data/sdub/sdub.pattern: [testng] 01:23:48,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:23:48,449 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,450 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-23_01-23-48.log] [testng] 01:23:48,450 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4911acaa - End of configuration. [testng] [2024-05-23 01:23:48,676] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne2.jpg: [testng] 01:23:48,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:23:48,677 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,678 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-23_01-23-48.log] [testng] 01:23:48,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3a9894c1 - End of configuration. [testng] [2024-05-23 01:23:48,691] [pool-1-thread-10] Initializing /data/10-31 E1/10-31 E1.tif: [testng] 01:23:48,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:23:48,692 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-23_01-23-48.log] [testng] 01:23:48,693 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1023f7fe - End of configuration. [testng] [2024-05-23 01:23:48,936] [pool-1-thread-9] Initializing /data/openjpeg/Bretagne2.j2k: [testng] 01:23:48,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:23:48,936 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,937 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-23_01-23-48.log] [testng] 01:23:48,938 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1fcced7 - End of configuration. [testng] [2024-05-23 01:23:48,965] [pool-1-thread-8] Initializing /data/openjpeg/Bretagne1.j2k: [testng] 01:23:48,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:23:48,965 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,966 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-23_01-23-48.log] [testng] 01:23:48,966 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b4c51ab - End of configuration. [testng] [2024-05-23 01:23:48,977] [pool-1-thread-7] Initializing /data/openjpeg/thumb_Cevennes2.jpg: [testng] 01:23:48,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:23:48,977 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:48,978 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-23_01-23-48.log] [testng] 01:23:48,978 |-INFO in ch.qos.logback.core.sift.SiftProcessor@528ff37b - End of configuration. [testng] [2024-05-23 01:23:49,002] [pool-1-thread-6] Initializing /data/openjpeg/Facade.pnm: [testng] 01:23:49,002 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:23:49,003 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,003 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-23_01-23-49.log] [testng] 01:23:49,004 |-INFO in ch.qos.logback.core.sift.SiftProcessor@679df212 - End of configuration. [testng] [2024-05-23 01:23:49,013] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes2.bmp: [testng] 01:23:49,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:23:49,014 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,014 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-23_01-23-49.log] [testng] 01:23:49,015 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44aa33ce - End of configuration. [testng] [2024-05-23 01:23:49,025] [pool-1-thread-4] Initializing /data/mouse-kidney/mouse-kidney.lif: [testng] 01:23:49,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:23:49,025 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,026 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-23_01-23-49.log] [testng] 01:23:49,027 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2cd12bf - End of configuration. [testng] [2024-05-23 01:23:49,112] [pool-1-thread-3] Initializing /data/openjpeg/Rome.jp2: [testng] 01:23:49,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:23:49,112 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,113 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-23_01-23-49.log] [testng] 01:23:49,113 |-INFO in ch.qos.logback.core.sift.SiftProcessor@29f3d44f - End of configuration. [testng] [2024-05-23 01:23:49,126] [pool-1-thread-2] Initializing /data/openjpeg/Bretagne1.ppm: [testng] 01:23:49,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:23:49,126 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:23:49,126 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-23_01-23-49.log] [testng] 01:23:49,127 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2ca780c5 - End of configuration. [testng] [2024-05-23 01:23:50,881] [pool-1-thread-7] Initializing /data/openjpeg/Bretagne2.ppm: [testng] [2024-05-23 01:23:50,891] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Bretagne1.jpg: [testng] [2024-05-23 01:23:50,902] [pool-1-thread-1] Initializing /data/openjpeg/FacadeERROPJ.bmp: [testng] [2024-05-23 01:23:50,925] [pool-1-thread-2] Initializing /data/ome/654Atemp.stk: [testng] [2024-05-23 01:23:51,047] [pool-1-thread-5] Initializing /data/openjpeg/Cevennes1.ppm: [testng] [2024-05-23 01:23:51,327] [pool-1-thread-11] Initializing /data/openjpeg/Rome.bmp: [testng] [2024-05-23 01:23:51,639] [pool-1-thread-12] Initializing /data/ome/011B1_Morph.HTD: [testng] [2024-05-23 01:23:52,541] [pool-1-thread-4] Initializing /data/openjpeg/Cevennes2.jp2: [testng] [2024-05-23 01:23:52,688] [pool-1-thread-6] Initializing /data/ome/t0_pos1-0_5x.lsm: [testng] [2024-05-23 01:23:53,025] [pool-1-thread-11] Initializing /data/ome/nfat10x3 good2_D12_w1.TIF: [testng] [2024-05-23 01:23:53,361] [pool-1-thread-2] Initializing /data/ome/tinyTest.d3d.dv: [testng] [2024-05-23 01:23:53,567] [pool-1-thread-10] Initializing /data/openjpeg/Cevennes1.j2k: [testng] [2024-05-23 01:23:53,585] [pool-1-thread-8] Initializing /data/ome/C1.lsm: [testng] [2024-05-23 01:23:53,717] [pool-1-thread-2] Initializing /data/ome/EXPERIMENT38_w1FITC_t1.STK: [testng] [2024-05-23 01:23:53,753] [pool-1-thread-11] Initializing /data/openjpeg/thumb_Rome.jpg: [testng] [2024-05-23 01:23:53,853] [pool-1-thread-7] Initializing /data/ome/C1midmusnorm.lsm: [testng] [2024-05-23 01:23:53,942] [pool-1-thread-5] Initializing /data/ome/anusgfpzs.lsm: [testng] [2024-05-23 01:23:54,046] [pool-1-thread-8] Initializing /data/openjpeg/Rome.ppm: [testng] [2024-05-23 01:23:54,073] [pool-1-thread-11] Initializing /data/ome/worm.tiff: [testng] [2024-05-23 01:23:54,190] [pool-1-thread-3] Initializing /data/openjpeg/thumb_Speedway.jpg: [testng] [2024-05-23 01:23:54,228] [pool-1-thread-4] Initializing /data/openjpeg/FacadeERROPJW.bmp: [testng] [2024-05-23 01:23:54,273] [pool-1-thread-6] Initializing /data/ome/PA-SDS-RFP-CenB_w1GFP_t1.stk: [testng] [2024-05-23 01:23:54,464] [pool-1-thread-2] Initializing /data/openjpeg/Cevennes2.ppm: [testng] [2024-05-23 01:23:54,473] [pool-1-thread-7] Initializing /data/openjpeg/Facade.bmp: [testng] [2024-05-23 01:23:54,513] [pool-1-thread-3] Initializing /data/kidney_TFl/kidney_TFl.pattern: [testng] [2024-05-23 01:23:54,584] [pool-1-thread-8] Initializing /data/ome/210502-0min-NFKB-4.r3d: [testng] [2024-05-23 01:23:54,780] [pool-1-thread-2] Initializing /data/openjpeg/thumb_Cevennes1.jpg: [testng] [2024-05-23 01:23:54,960] [pool-1-thread-5] Initializing /data/TAABA/TAABA.pattern: [testng] [2024-05-23 01:23:56,451] [pool-1-thread-2] Initializing /data/ome/C1lowmusgfp.lsm: [testng] [2024-05-23 01:23:56,490] [pool-1-thread-1] Initializing /data/ome/Cmidmusgfp1.lsm: [testng] [2024-05-23 01:23:56,702] [pool-1-thread-3] Initializing /data/ome/cb_1.r3d: [testng] [2024-05-23 01:23:56,938] [pool-1-thread-2] Initializing /data/ome/Adultmidsection.lsm: [testng] [2024-05-23 01:23:56,992] [pool-1-thread-6] Initializing /data/openjpeg/Bretagne2.bmp: [testng] [2024-05-23 01:23:56,999] [pool-1-thread-1] Initializing /data/ome/embryo.lsm: [testng] [2024-05-23 01:23:57,258] [pool-1-thread-8] Initializing /data/ome/tiffany.color.tiff: [testng] [2024-05-23 01:23:57,604] [pool-1-thread-2] Initializing /data/ome/Cpharynxzs1.lsm: [testng] [2024-05-23 01:23:57,749] [pool-1-thread-1] Initializing /data/ome/n2_plate18_P24_w1.tif: [testng] [2024-05-23 01:23:58,002] [pool-1-thread-3] Initializing /data/ome/nfat10x3 good2_D12_w3.TIF: [testng] [2024-05-23 01:23:58,183] [pool-1-thread-8] Initializing /data/ome/CHOBI_d3d.dv: [testng] [2024-05-23 01:23:58,376] [pool-1-thread-1] Initializing /data/openjpeg/Cevennes1.bmp: [testng] [2024-05-23 01:23:58,445] [pool-1-thread-2] Initializing /data/ome/t1_pos1-0_5x.lsm: [testng] [2024-05-23 01:23:58,745] [pool-1-thread-8] Initializing /data/ome/arwen0205_raw00201.pic: [testng] [2024-05-23 01:23:58,815] [pool-1-thread-3] Initializing /data/openjpeg/thumb_facade.jpg: [testng] [2024-05-23 01:23:58,978] [pool-1-thread-11] Initializing /data/openjpeg/Bretagne1.bmp: [testng] [2024-05-23 01:23:59,032] [pool-1-thread-7] Initializing /data/ome/nfat10x3 good2_D12_w2.TIF: [testng] [2024-05-23 01:23:59,156] [pool-1-thread-3] Initializing /data/ome/PA-tub-wtmcakthurs-5_w1GFP_t1.STK: [testng] [2024-05-23 01:23:59,255] [pool-1-thread-4] Initializing /data/ome/compressed2ChZ.lsm: [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 11 seconds Finished: SUCCESS